Job ID = 6497573 SRX = SRX747299 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:26:12 prefetch.2.10.7: 1) Downloading 'SRR1634997'... 2020-06-25T22:26:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:27:30 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:27:31 prefetch.2.10.7: 'SRR1634997' is valid 2020-06-25T22:27:31 prefetch.2.10.7: 1) 'SRR1634997' was downloaded successfully 2020-06-25T22:28:03 prefetch.2.10.7: 'SRR1634997' has 6 unresolved dependencies 2020-06-25T22:28:03 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-25T22:28:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:37:45 prefetch.2.10.7: HTTPS download failed 2020-06-25T22:37:45 prefetch.2.10.7: 2) failed to download ncbi-acc:BX284601.4?vdb-ctx=refseq 2020-06-25T22:45:25 fastq-dump.2.10.7 err: transfer canceled while allocating buffer within file system module - Cannot KHttpFileTimedReadChunked Read 16538802 spots for SRR1634997/SRR1634997.sra Written 16538802 spots for SRR1634997/SRR1634997.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:42 16538802 reads; of these: 16538802 (100.00%) were unpaired; of these: 1446424 (8.75%) aligned 0 times 12432739 (75.17%) aligned exactly 1 time 2659639 (16.08%) aligned >1 times 91.25% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 2430438 / 15092378 = 0.1610 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:54:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 07:54:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:54:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:54:55: 1000000 INFO @ Fri, 26 Jun 2020 07:55:01: 2000000 INFO @ Fri, 26 Jun 2020 07:55:07: 3000000 INFO @ Fri, 26 Jun 2020 07:55:13: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:55:19: 5000000 INFO @ Fri, 26 Jun 2020 07:55:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 07:55:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:55:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:55:25: 6000000 INFO @ Fri, 26 Jun 2020 07:55:25: 1000000 INFO @ Fri, 26 Jun 2020 07:55:31: 7000000 INFO @ Fri, 26 Jun 2020 07:55:32: 2000000 INFO @ Fri, 26 Jun 2020 07:55:38: 8000000 INFO @ Fri, 26 Jun 2020 07:55:38: 3000000 INFO @ Fri, 26 Jun 2020 07:55:44: 9000000 INFO @ Fri, 26 Jun 2020 07:55:44: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:55:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 07:55:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:55:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:55:50: 10000000 INFO @ Fri, 26 Jun 2020 07:55:50: 5000000 INFO @ Fri, 26 Jun 2020 07:55:55: 1000000 INFO @ Fri, 26 Jun 2020 07:55:57: 6000000 INFO @ Fri, 26 Jun 2020 07:55:57: 11000000 INFO @ Fri, 26 Jun 2020 07:56:02: 2000000 INFO @ Fri, 26 Jun 2020 07:56:03: 7000000 INFO @ Fri, 26 Jun 2020 07:56:03: 12000000 INFO @ Fri, 26 Jun 2020 07:56:07: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:56:07: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:56:07: #1 total tags in treatment: 12661940 INFO @ Fri, 26 Jun 2020 07:56:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:56:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:56:08: #1 tags after filtering in treatment: 12661940 INFO @ Fri, 26 Jun 2020 07:56:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:56:08: #1 finished! INFO @ Fri, 26 Jun 2020 07:56:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:56:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:56:08: 3000000 INFO @ Fri, 26 Jun 2020 07:56:09: #2 number of paired peaks: 252 WARNING @ Fri, 26 Jun 2020 07:56:09: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Fri, 26 Jun 2020 07:56:09: start model_add_line... INFO @ Fri, 26 Jun 2020 07:56:09: start X-correlation... INFO @ Fri, 26 Jun 2020 07:56:09: end of X-cor INFO @ Fri, 26 Jun 2020 07:56:09: #2 finished! INFO @ Fri, 26 Jun 2020 07:56:09: #2 predicted fragment length is 32 bps INFO @ Fri, 26 Jun 2020 07:56:09: #2 alternative fragment length(s) may be 2,32,538 bps INFO @ Fri, 26 Jun 2020 07:56:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.05_model.r WARNING @ Fri, 26 Jun 2020 07:56:09: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:56:09: #2 You may need to consider one of the other alternative d(s): 2,32,538 WARNING @ Fri, 26 Jun 2020 07:56:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:56:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:56:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:56:09: 8000000 INFO @ Fri, 26 Jun 2020 07:56:15: 4000000 INFO @ Fri, 26 Jun 2020 07:56:16: 9000000 INFO @ Fri, 26 Jun 2020 07:56:21: 5000000 INFO @ Fri, 26 Jun 2020 07:56:22: 10000000 INFO @ Fri, 26 Jun 2020 07:56:27: 6000000 INFO @ Fri, 26 Jun 2020 07:56:28: 11000000 INFO @ Fri, 26 Jun 2020 07:56:34: 12000000 INFO @ Fri, 26 Jun 2020 07:56:34: 7000000 INFO @ Fri, 26 Jun 2020 07:56:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:56:38: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:56:38: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:56:38: #1 total tags in treatment: 12661940 INFO @ Fri, 26 Jun 2020 07:56:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:56:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:56:38: #1 tags after filtering in treatment: 12661940 INFO @ Fri, 26 Jun 2020 07:56:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:56:38: #1 finished! INFO @ Fri, 26 Jun 2020 07:56:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:56:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:56:39: #2 number of paired peaks: 252 WARNING @ Fri, 26 Jun 2020 07:56:39: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Fri, 26 Jun 2020 07:56:39: start model_add_line... INFO @ Fri, 26 Jun 2020 07:56:39: start X-correlation... INFO @ Fri, 26 Jun 2020 07:56:39: end of X-cor INFO @ Fri, 26 Jun 2020 07:56:39: #2 finished! INFO @ Fri, 26 Jun 2020 07:56:39: #2 predicted fragment length is 32 bps INFO @ Fri, 26 Jun 2020 07:56:39: #2 alternative fragment length(s) may be 2,32,538 bps INFO @ Fri, 26 Jun 2020 07:56:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.10_model.r WARNING @ Fri, 26 Jun 2020 07:56:39: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:56:39: #2 You may need to consider one of the other alternative d(s): 2,32,538 WARNING @ Fri, 26 Jun 2020 07:56:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:56:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:56:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:56:40: 8000000 INFO @ Fri, 26 Jun 2020 07:56:46: 9000000 INFO @ Fri, 26 Jun 2020 07:56:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:56:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:56:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.05_summits.bed INFO @ Fri, 26 Jun 2020 07:56:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (689 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:56:52: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:56:58: 11000000 INFO @ Fri, 26 Jun 2020 07:57:04: 12000000 INFO @ Fri, 26 Jun 2020 07:57:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:57:08: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:57:08: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:57:08: #1 total tags in treatment: 12661940 INFO @ Fri, 26 Jun 2020 07:57:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:57:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:57:09: #1 tags after filtering in treatment: 12661940 INFO @ Fri, 26 Jun 2020 07:57:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:57:09: #1 finished! INFO @ Fri, 26 Jun 2020 07:57:09: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:57:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:57:09: #2 number of paired peaks: 252 WARNING @ Fri, 26 Jun 2020 07:57:09: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Fri, 26 Jun 2020 07:57:09: start model_add_line... INFO @ Fri, 26 Jun 2020 07:57:10: start X-correlation... INFO @ Fri, 26 Jun 2020 07:57:10: end of X-cor INFO @ Fri, 26 Jun 2020 07:57:10: #2 finished! INFO @ Fri, 26 Jun 2020 07:57:10: #2 predicted fragment length is 32 bps INFO @ Fri, 26 Jun 2020 07:57:10: #2 alternative fragment length(s) may be 2,32,538 bps INFO @ Fri, 26 Jun 2020 07:57:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.20_model.r WARNING @ Fri, 26 Jun 2020 07:57:10: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:57:10: #2 You may need to consider one of the other alternative d(s): 2,32,538 WARNING @ Fri, 26 Jun 2020 07:57:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:57:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:57:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:57:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:57:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:57:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.10_summits.bed INFO @ Fri, 26 Jun 2020 07:57:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (281 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:57:35: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:57:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:57:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:57:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747299/SRX747299.20_summits.bed INFO @ Fri, 26 Jun 2020 07:57:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (95 records, 4 fields): 2 millis CompletedMACS2peakCalling