Any idea what's going wring I have made it to this point and stuck again, would you advice
/root/miniconda/envs/xtea_env/lib/python3.7/site-packages/sklearn/externals/joblib/externals/cloudpickle/cloudpickle.py:47: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
import imp
/root/miniconda/envs/xtea_env/lib/python3.7/site-packages/sklearn/ensemble/gradient_boosting.py:34: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
from ._gradient_boosting import predict_stages
/root/miniconda/envs/xtea_env/lib/python3.7/site-packages/sklearn/ensemble/gradient_boosting.py:34: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
from ._gradient_boosting import predict_stages
Working on "clip" step!
Ave coverage is 10.284: automatic parameters (clip, disc, clip-disc) with value (2, 3 ,0)
Clip cutoff: 2, 2, 0 are used!!!
Input bam /cromwell_root/fc-00bcc31d-9daf-40fa-bca6-2c6aa332a71c/NDX-22-829-004.bam is sequenced from illumina platform!
Running command: mkdir -p ./workingdir/NDX-22-829-004/pub_clip/0/
Running command: mkdir -p ./workingdir/NDX-22-829-004/L1/tmp/clip/0/
Collected clipped reads file ./workingdir/NDX-22-829-004/pub_clip/0/NDX-22-829-004.bam.clipped.fq doesn't exist. Generate it now!
Initial minimum clip cutoff is 2
('Output info: Collect clipped parts for file ', '/cromwell_root/fc-00bcc31d-9daf-40fa-bca6-2c6aa332a71c/NDX-22-829-004.bam')
Skip chromosome chrM
Skip chromosome chr1_KI270706v1_random
Skip chromosome chr1_KI270707v1_random
Skip chromosome chr1_KI270708v1_random
Skip chromosome chr1_KI270709v1_random
Skip chromosome chr1_KI270710v1_random
Skip chromosome chr1_KI270711v1_random
Skip chromosome chr1_KI270712v1_random
Skip chromosome chr1_KI270713v1_random
Skip chromosome chr1_KI270714v1_random
Skip chromosome chr2_KI270715v1_random
Skip chromosome chr2_KI270716v1_random
Skip chromosome chr3_GL000221v1_random
Skip chromosome chr4_GL000008v2_random
Skip chromosome chr5_GL000208v1_random
Skip chromosome chr9_KI270717v1_random
Skip chromosome chr9_KI270718v1_random
Skip chromosome chr9_KI270719v1_random
Skip chromosome chr9_KI270720v1_random
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Long List.
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Skip chromosome HLA-DRB1*15:01:01:04
Skip chromosome HLA-DRB1*15:02:01
Skip chromosome HLA-DRB1*15:03:01:01
Skip chromosome HLA-DRB1*15:03:01:02
Skip chromosome HLA-DRB1*16:02:01
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[E::main_mem] fail to open file `./workingdir/NDX-22-829-004/pub_clip/0/NDX-22-829-004.bam.clipped.fq'.
Running command: ln -s ./workingdir/NDX-22-829-004/L1/tmp/clip/0/NDX-22-829-004.bam.clipped.fq ./workingdir/NDX-22-829-004/pub_clip/0/NDX-22-829-004.bam.clipped.fq
('Output info: Re-align clipped parts for file ', '/cromwell_root/fc-00bcc31d-9daf-40fa-bca6-2c6aa332a71c/NDX-22-829-004.bam')
Running command: bwa mem -t 7 -T 9 -k 9 -o ./workingdir/NDX-22-829-004/L1/tmp/NDX-22-829-004.bam.clipped.sam_cns.sam /cromwell_root/fc-00bcc31d-9daf-40fa-bca6-2c6aa332a71c/rep_lib_annotation/consensus/LINE1.fa ./workingdir/NDX-22-829-004/pub_clip/0/NDX-22-829-004.bam.clipped.fq
Traceback (most recent call last):
File "/root/miniconda/envs/xtea_env/lib/x_TEA_main.py", line 526, in <module>
wfolder_pub_clip, b_force, max_cov_cutoff, sf_out)
File "/root/miniconda/envs/xtea_env/lib/x_TEI_locator.py", line 109, in call_TEI_candidate_sites_from_multiple_alignmts
sf_new_pub, i_idx_bam, b_force, max_cov, sf_out_tmp)
File "/root/miniconda/envs/xtea_env/lib/x_TEI_locator.py", line 633, in call_TEI_candidate_sites_from_clip_reads_v2
bwa_align.two_stage_realign(sf_rep_cns, sf_ref, sf_all_clip_fq, sf_algnmt)
File "/root/miniconda/envs/xtea_env/lib/bwa_align.py", line 263, in two_stage_realign
self.get_fully_mapped_algnmts(sf_sam_cns, sf_ref_cns, max_clip_len, sf_fully_sam, sf_unmap_fa, sf_polyA_fa)
File "/root/miniconda/envs/xtea_env/lib/bwa_align.py", line 167, in get_fully_mapped_algnmts
bamfile = pysam.AlignmentFile(sf_sam, "r", reference_filename=sf_reference) #
File "pysam/libcalignmentfile.pyx", line 741, in pysam.libcalignmentfile.AlignmentFile.__cinit__
File "pysam/libcalignmentfile.pyx", line 990, in pysam.libcalignmentfile.AlignmentFile._open
ValueError: file has no sequences defined (mode='r') - is it SAM/BAM format? Consider opening with check_sq=False
Any idea what's going wring I have made it to this point and stuck again, would you advice