Job ID = 6497363 SRX = SRX277028 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:40:38 prefetch.2.10.7: 1) Downloading 'SRR849697'... 2020-06-25T21:40:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:41:14 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:41:15 prefetch.2.10.7: 'SRR849697' is valid 2020-06-25T21:41:15 prefetch.2.10.7: 1) 'SRR849697' was downloaded successfully Read 6772854 spots for SRR849697/SRR849697.sra Written 6772854 spots for SRR849697/SRR849697.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: 00:00:01 Multiseed full-index search: 00:01:04 6772854 reads; of these: 6772854 (100.00%) were unpaired; of these: 176117 (2.60%) aligned 0 times 5321344 (78.57%) aligned exactly 1 time 1275393 (18.83%) aligned >1 times 97.40% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 589642 / 6596737 = 0.0894 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 06:44:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.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 06:44:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:44:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:44:51: 1000000 INFO @ Fri, 26 Jun 2020 06:44:56: 2000000 INFO @ Fri, 26 Jun 2020 06:45:02: 3000000 INFO @ Fri, 26 Jun 2020 06:45:07: 4000000 INFO @ Fri, 26 Jun 2020 06:45:12: 5000000 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 06:45:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.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 06:45:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:45:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:45:17: 6000000 INFO @ Fri, 26 Jun 2020 06:45:17: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 06:45:17: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 06:45:17: #1 total tags in treatment: 6007095 INFO @ Fri, 26 Jun 2020 06:45:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:45:17: #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 06:45:17: #1 tags after filtering in treatment: 6007095 INFO @ Fri, 26 Jun 2020 06:45:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:45:17: #1 finished! INFO @ Fri, 26 Jun 2020 06:45:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:45:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:45:17: #2 number of paired peaks: 438 WARNING @ Fri, 26 Jun 2020 06:45:17: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Fri, 26 Jun 2020 06:45:17: start model_add_line... INFO @ Fri, 26 Jun 2020 06:45:17: start X-correlation... INFO @ Fri, 26 Jun 2020 06:45:17: end of X-cor INFO @ Fri, 26 Jun 2020 06:45:17: #2 finished! INFO @ Fri, 26 Jun 2020 06:45:17: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 06:45:17: #2 alternative fragment length(s) may be 2,40,564 bps INFO @ Fri, 26 Jun 2020 06:45:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.05_model.r WARNING @ Fri, 26 Jun 2020 06:45:17: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:45:17: #2 You may need to consider one of the other alternative d(s): 2,40,564 WARNING @ Fri, 26 Jun 2020 06:45:17: #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 06:45:17: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:45:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:45:21: 1000000 INFO @ Fri, 26 Jun 2020 06:45:25: 2000000 INFO @ Fri, 26 Jun 2020 06:45:29: 3000000 INFO @ Fri, 26 Jun 2020 06:45:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:45:34: 4000000 INFO @ Fri, 26 Jun 2020 06:45:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:45:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:45:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.05_summits.bed INFO @ Fri, 26 Jun 2020 06:45:38: Done! INFO @ Fri, 26 Jun 2020 06:45:38: 5000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (493 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:45:43: 6000000 INFO @ Fri, 26 Jun 2020 06:45:43: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 06:45:43: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 06:45:43: #1 total tags in treatment: 6007095 INFO @ Fri, 26 Jun 2020 06:45:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:45:43: #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 06:45:43: #1 tags after filtering in treatment: 6007095 INFO @ Fri, 26 Jun 2020 06:45:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:45:43: #1 finished! INFO @ Fri, 26 Jun 2020 06:45:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:45:43: #2 number of paired peaks: 438 WARNING @ Fri, 26 Jun 2020 06:45:43: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Fri, 26 Jun 2020 06:45:43: start model_add_line... INFO @ Fri, 26 Jun 2020 06:45:44: start X-correlation... INFO @ Fri, 26 Jun 2020 06:45:44: end of X-cor INFO @ Fri, 26 Jun 2020 06:45:44: #2 finished! INFO @ Fri, 26 Jun 2020 06:45:44: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 06:45:44: #2 alternative fragment length(s) may be 2,40,564 bps INFO @ Fri, 26 Jun 2020 06:45:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.10_model.r WARNING @ Fri, 26 Jun 2020 06:45:44: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:45:44: #2 You may need to consider one of the other alternative d(s): 2,40,564 WARNING @ Fri, 26 Jun 2020 06:45:44: #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 06:45:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:45:44: #3 Pre-compute pvalue-qvalue table... 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 06:45:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.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 06:45:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:45:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:45:51: 1000000 INFO @ Fri, 26 Jun 2020 06:45:55: 2000000 INFO @ Fri, 26 Jun 2020 06:45:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:45:59: 3000000 INFO @ Fri, 26 Jun 2020 06:46:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.10_peaks.xls INFO @ Fri, 26 Jun 2020 06:46:04: 4000000 INFO @ Fri, 26 Jun 2020 06:46:08: 5000000 BedGraph に変換しました。 INFO @ Fri, 26 Jun 2020 06:46:12: 6000000 INFO @ Fri, 26 Jun 2020 06:46:13: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 06:46:13: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 06:46:13: #1 total tags in treatment: 6007095 INFO @ Fri, 26 Jun 2020 06:46:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:46:13: #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 06:46:13: #1 tags after filtering in treatment: 6007095 INFO @ Fri, 26 Jun 2020 06:46:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:46:13: #1 finished! INFO @ Fri, 26 Jun 2020 06:46:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:46:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:46:13: #2 number of paired peaks: 438 WARNING @ Fri, 26 Jun 2020 06:46:13: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Fri, 26 Jun 2020 06:46:13: start model_add_line... INFO @ Fri, 26 Jun 2020 06:46:13: start X-correlation... INFO @ Fri, 26 Jun 2020 06:46:13: end of X-cor INFO @ Fri, 26 Jun 2020 06:46:13: #2 finished! INFO @ Fri, 26 Jun 2020 06:46:13: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 06:46:13: #2 alternative fragment length(s) may be 2,40,564 bps INFO @ Fri, 26 Jun 2020 06:46:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.20_model.r INFO @ Fri, 26 Jun 2020 06:46:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:46:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.10_summits.bed INFO @ Fri, 26 Jun 2020 06:46:28: Done! BigWig に変換中... WARNING @ Fri, 26 Jun 2020 06:46:28: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:46:28: #2 You may need to consider one of the other alternative d(s): 2,40,564 WARNING @ Fri, 26 Jun 2020 06:46:28: #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 06:46:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:46:28: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (216 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:46:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 06:46:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:46:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:46:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277028/SRX277028.20_summits.bed INFO @ Fri, 26 Jun 2020 06:46:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (59 records, 4 fields): 102 millis CompletedMACS2peakCalling