error when test data

[ch8316f5eyu]

I used conda to install RelocaTE2. When I bash run_test.sh, error occurred：
(RelocaTE2) gmb23@bio3-2288H-V5:~/miniconda3/envs/RelocaTE2/test_data$ bash run_test.sh /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads fastq Reference need to be indexed by bwa: /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.fa [bwa_index] Pack FASTA... 0.03 sec [bwa_index] Construct BWT for the packed sequence... [bwa_index] 0.41 seconds elapse. [bwa_index] Update BWT... 0.01 sec [bwa_index] Pack forward-only FASTA... 0.01 sec [bwa_index] Construct SA from BWT and Occ... 0.19 sec [main] Version: 0.6.2-r126 [main] CMD: /home/data/gmb23/miniconda3/envs/RelocaTE2/bin/bwa index /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.fa [main] Real time: 0.672 sec; CPU: 0.667 sec job: sh /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/shellscripts/step_2/0.fq2fa.sh job: sh /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/shellscripts/step_2/1.fq2fa.sh job: sh /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/shellscripts/step_3/0.te_repeat.blat.sh job: sh /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/shellscripts/step_3/1.te_repeat.blat.sh /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/flanking_seq/MSU7.Chr3_2M.ALL_reads_6X_100_500_2.te_repeat.flankingReads.fq p2 /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/flanking_seq/MSU7.Chr3_2M.ALL_reads_6X_100_500_1.te_repeat.flankingReads.fq p1 pair1: /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/flanking_seq/MSU7.Chr3_2M.ALL_reads_6X_100_500_1.te_repeat.flankingReads.fq; pair2: /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/flanking_seq/MSU7.Chr3_2M.ALL_reads_6X_100_500_2.te_repeat.flankingReads.fq testing if bam exists: /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/bwa_aln/MSU7.Chr3_2M.MSU7.Chr3_2M.ALL_reads_6X_100_500_1.te_repeat.flankingReads.bwa.mates.bam pre: /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/flanking_seq/MSU7.Chr3_2M.ALL_reads_6X_100_500 bam not exists, preceed with bwa to map the reads /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/flanking_seq/MSU7.Chr3_2M.ALL_reads_6X_100_500_1.te_repeat.flankingReads.fq /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/flanking_seq/MSU7.Chr3_2M.ALL_reads_6X_100_500_2.te_repeat.flankingReads.fq /home/data/gmb23/miniconda3/envs/RelocaTE2/scripts/clean_pairs_memory.py --fq1 /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/flanking_seq/MSU7.Chr3_2M.ALL_reads_6X_100_500_1.te_repeat.flankingReads.fq --fq2 /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/flanking_seq/MSU7.Chr3_2M.ALL_reads_6X_100_500_2.te_repeat.flankingReads.fq --repeat /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/te_containing_fq --fq_dir /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads --seqtk /home/data/gmb23/miniconda3/envs/RelocaTE2/bin/seqtk [bwa_sai2sam_pe_core] convert to sequence coordinate... [infer_isize] (25, 50, 75) percentile: (355, 432, 511) [infer_isize] low and high boundaries: 100 and 823 for estimating avg and std [infer_isize] inferred external isize from 1002 pairs: 426.123 +/- 120.313 [infer_isize] skewness: -0.378; kurtosis: 0.077; ap_prior: 1.00e-05 [infer_isize] inferred maximum insert size: 1114 (5.72 sigma) [bwa_sai2sam_pe_core] time elapses: 0.02 sec [bwa_sai2sam_pe_core] changing coordinates of 40 alignments. [bwa_sai2sam_pe_core] align unmapped mate... [bwa_paired_sw] 11 out of 13 Q17 singletons are mated. [bwa_paired_sw] 0 out of 0 Q17 discordant pairs are fixed. [bwa_sai2sam_pe_core] time elapses: 0.01 sec [bwa_sai2sam_pe_core] refine gapped alignments... 0.00 sec [bwa_sai2sam_pe_core] print alignments... [vfprintf(stdout)] Broken pipe Abort! Aborted (core dumped) Traceback (most recent call last): File "/home/data/gmb23/miniconda3/envs/RelocaTE2/scripts/relocaTE_align.py", line 631, in <module> main() File "/home/data/gmb23/miniconda3/envs/RelocaTE2/scripts/relocaTE_align.py", line 624, in main map_reads_bwa(scripts, flanking_fq, path, genome_file, fastq_dir, target, bwa, samtools, seqtk, cpu, mate_file) File "/home/data/gmb23/miniconda3/envs/RelocaTE2/scripts/relocaTE_align.py", line 404, in map_reads_bwa collect_files = multiprocess_pool(parameters, cpu) File "/home/data/gmb23/miniconda3/envs/RelocaTE2/scripts/relocaTE_align.py", line 364, in multiprocess_pool imap_it = pool.map(map_reads_bwa_mp_helper, tuple(parameters)) File "/home/data/gmb23/miniconda3/envs/RelocaTE2/lib/python2.7/multiprocessing/pool.py", line 251, in map return self.map_async(func, iterable, chunksize).get() File "/home/data/gmb23/miniconda3/envs/RelocaTE2/lib/python2.7/multiprocessing/pool.py", line 567, in get raise self._value ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_seq=True job: sh /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/shellscripts/step_4/step_4.MSU7.Chr3_2M.repeat.align.sh Step5: Find non-reference insertions find insertions on Chr3 fullread bam: /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/bwa_aln/MSU7.Chr3_2M.repeat.fullreads.bwa.sorted.bam Traceback (most recent call last): File "/home/data/gmb23/miniconda3/envs/RelocaTE2/scripts/relocaTE_insertionFinder.py", line 1825, in <module> main() File "/home/data/gmb23/miniconda3/envs/RelocaTE2/scripts/relocaTE_insertionFinder.py", line 1809, in main read_junction_reads_align(align_file_f, read_repeat, teJunctionReads) File "/home/data/gmb23/miniconda3/envs/RelocaTE2/scripts/relocaTE_insertionFinder.py", line 1648, in read_junction_reads_align fsam = pysam.AlignmentFile(align_file_f, 'rb') File "pysam/calignmentfile.pyx", line 333, in pysam.calignmentfile.AlignmentFile.__cinit__ (pysam/calignmentfile.c:4808) File "pysam/calignmentfile.pyx", line 533, in pysam.calignmentfile.AlignmentFile._open (pysam/calignmentfile.c:7027) IOError: file /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/bwa_aln/MSU7.Chr3_2M.repeat.fullreads.bwa.sorted.bamnot found job: sh /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/shellscripts/step_5/0.repeat.findSites.sh Step6: Find reference insertions Traceback (most recent call last): File "/home/data/gmb23/miniconda3/envs/RelocaTE2/scripts/relocaTE_absenceFinder.py", line 967, in <module> main() File "/home/data/gmb23/miniconda3/envs/RelocaTE2/scripts/relocaTE_absenceFinder.py", line 960, in main find_insertion_cluster_bam(align_file, read_repeat, usr_target, TSD, teInsertions, teInsertions_reads, teReadClusters, teReadClusters_count, teReadClusters_depth, existingTE_intact, existingTE_found, teSupportingReads) File "/home/data/gmb23/miniconda3/envs/RelocaTE2/scripts/relocaTE_absenceFinder.py", line 822, in find_insertion_cluster_bam fsam = pysam.AlignmentFile(align_file, 'rb') File "pysam/calignmentfile.pyx", line 333, in pysam.calignmentfile.AlignmentFile.__cinit__ (pysam/calignmentfile.c:4808) File "pysam/calignmentfile.pyx", line 533, in pysam.calignmentfile.AlignmentFile._open (pysam/calignmentfile.c:7027) IOError: file/home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/bwa_aln/MSU7.Chr3_2M.repeat.bwa.sorted.bamnot found job: sh /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/shellscripts/step_6/0.repeat.absence.sh /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/shellscripts/step_7/0.repeat.characterize.sh: 1: cannot create /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/results/ALL.all_nonref_insert.gff: Directory nonexistent /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/shellscripts/step_7/0.repeat.characterize.sh: 2: cannot create /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/results/ALL.all_nonref_insert.txt: Directory nonexistent cat: '/home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/results/*.all_nonref_insert.txt': No such file or directory sh: 1: cannot create /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/results/ALL.all_nonref_insert.overlap: Directory nonexistent /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/shellscripts/step_7/0.repeat.characterize.sh: 4: cannot create /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/results/ALL.all_ref_insert.txt: Directory nonexistent /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/shellscripts/step_7/0.repeat.characterize.sh: 5: cannot create /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/results/ALL.all_ref_insert.gff: Directory nonexistent cannot open /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/results/ALL.all_nonref_insert.txt No such file or directory job: sh /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/shellscripts/step_7/0.repeat.characterize.sh rm: cannot remove '/home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/repeat/fastq_split': No such file or directory job: sh /home/data/gmb23/miniconda3/envs/RelocaTE2/test_data/MSU7.Chr3_2M.ALL_reads_RelocaTE2_outdir/clean_intermediate_files.sh Start: 1614121859 End: 1614121870 Run time: 11 Done
Any ideas?
It's weird this error didn't occurred in the first time. Because my conda was broken, I reinstalled conda and relocate2, the error occurred.