Job ID = 6497438 SRX = SRX494936 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:39:05 prefetch.2.10.7: 1) Downloading 'SRR1198468'... 2020-06-25T22:39:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:41:08 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:41:08 prefetch.2.10.7: 1) 'SRR1198468' was downloaded successfully Read 23003577 spots for SRR1198468/SRR1198468.sra Written 23003577 spots for SRR1198468/SRR1198468.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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:29 23003577 reads; of these: 23003577 (100.00%) were unpaired; of these: 1607531 (6.99%) aligned 0 times 17615775 (76.58%) aligned exactly 1 time 3780271 (16.43%) aligned >1 times 93.01% overall alignment rate Time searching: 00:05:30 Overall time: 00:05:30 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_sort_core] merging from 12 files... [bam_rmdupse_core] 13810760 / 21396046 = 0.6455 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 07:52:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.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 07:52:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:52:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:52:23: 1000000 INFO @ Fri, 26 Jun 2020 07:52:28: 2000000 INFO @ Fri, 26 Jun 2020 07:52:34: 3000000 INFO @ Fri, 26 Jun 2020 07:52:39: 4000000 INFO @ Fri, 26 Jun 2020 07:52:45: 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 07:52:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.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 07:52:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:52:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:52:50: 6000000 INFO @ Fri, 26 Jun 2020 07:52:53: 1000000 INFO @ Fri, 26 Jun 2020 07:52:56: 7000000 INFO @ Fri, 26 Jun 2020 07:52:59: 2000000 INFO @ Fri, 26 Jun 2020 07:52:59: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:52:59: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:52:59: #1 total tags in treatment: 7585286 INFO @ Fri, 26 Jun 2020 07:52:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:52:59: #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 07:53:00: #1 tags after filtering in treatment: 7585286 INFO @ Fri, 26 Jun 2020 07:53:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:53:00: #1 finished! INFO @ Fri, 26 Jun 2020 07:53:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:53:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:53:00: #2 number of paired peaks: 646 WARNING @ Fri, 26 Jun 2020 07:53:00: Fewer paired peaks (646) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 646 pairs to build model! INFO @ Fri, 26 Jun 2020 07:53:00: start model_add_line... INFO @ Fri, 26 Jun 2020 07:53:00: start X-correlation... INFO @ Fri, 26 Jun 2020 07:53:00: end of X-cor INFO @ Fri, 26 Jun 2020 07:53:00: #2 finished! INFO @ Fri, 26 Jun 2020 07:53:00: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 07:53:00: #2 alternative fragment length(s) may be 3,47 bps INFO @ Fri, 26 Jun 2020 07:53:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.05_model.r WARNING @ Fri, 26 Jun 2020 07:53:00: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:53:00: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Fri, 26 Jun 2020 07:53:00: #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 07:53:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:53:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:53:05: 3000000 INFO @ Fri, 26 Jun 2020 07:53:11: 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 07:53:16: 5000000 INFO @ Fri, 26 Jun 2020 07:53:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.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 07:53:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:53:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:53:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:53:22: 6000000 INFO @ Fri, 26 Jun 2020 07:53:24: 1000000 INFO @ Fri, 26 Jun 2020 07:53:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:53:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:53:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.05_summits.bed INFO @ Fri, 26 Jun 2020 07:53:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (851 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:53:28: 7000000 INFO @ Fri, 26 Jun 2020 07:53:31: 2000000 INFO @ Fri, 26 Jun 2020 07:53:32: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:53:32: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:53:32: #1 total tags in treatment: 7585286 INFO @ Fri, 26 Jun 2020 07:53:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:53:32: #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 07:53:32: #1 tags after filtering in treatment: 7585286 INFO @ Fri, 26 Jun 2020 07:53:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:53:32: #1 finished! INFO @ Fri, 26 Jun 2020 07:53:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:53:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:53:32: #2 number of paired peaks: 646 WARNING @ Fri, 26 Jun 2020 07:53:32: Fewer paired peaks (646) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 646 pairs to build model! INFO @ Fri, 26 Jun 2020 07:53:32: start model_add_line... INFO @ Fri, 26 Jun 2020 07:53:33: start X-correlation... INFO @ Fri, 26 Jun 2020 07:53:33: end of X-cor INFO @ Fri, 26 Jun 2020 07:53:33: #2 finished! INFO @ Fri, 26 Jun 2020 07:53:33: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 07:53:33: #2 alternative fragment length(s) may be 3,47 bps INFO @ Fri, 26 Jun 2020 07:53:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.10_model.r WARNING @ Fri, 26 Jun 2020 07:53:33: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:53:33: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Fri, 26 Jun 2020 07:53:33: #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 07:53:33: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:53:37: 3000000 INFO @ Fri, 26 Jun 2020 07:53:44: 4000000 INFO @ Fri, 26 Jun 2020 07:53:50: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:53:50: 5000000 INFO @ Fri, 26 Jun 2020 07:53:56: 6000000 INFO @ Fri, 26 Jun 2020 07:53:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:53:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:53:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.10_summits.bed INFO @ Fri, 26 Jun 2020 07:53:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (565 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:54:03: 7000000 INFO @ Fri, 26 Jun 2020 07:54:06: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:54:06: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:54:06: #1 total tags in treatment: 7585286 INFO @ Fri, 26 Jun 2020 07:54:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:54:06: #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 07:54:07: #1 tags after filtering in treatment: 7585286 INFO @ Fri, 26 Jun 2020 07:54:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:54:07: #1 finished! INFO @ Fri, 26 Jun 2020 07:54:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:54:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:54:07: #2 number of paired peaks: 646 WARNING @ Fri, 26 Jun 2020 07:54:07: Fewer paired peaks (646) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 646 pairs to build model! INFO @ Fri, 26 Jun 2020 07:54:07: start model_add_line... INFO @ Fri, 26 Jun 2020 07:54:07: start X-correlation... INFO @ Fri, 26 Jun 2020 07:54:07: end of X-cor INFO @ Fri, 26 Jun 2020 07:54:07: #2 finished! INFO @ Fri, 26 Jun 2020 07:54:07: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 07:54:07: #2 alternative fragment length(s) may be 3,47 bps INFO @ Fri, 26 Jun 2020 07:54:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.20_model.r WARNING @ Fri, 26 Jun 2020 07:54:07: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:54:07: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Fri, 26 Jun 2020 07:54:07: #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 07:54:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:54:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:54:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:54:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:54:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:54:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494936/SRX494936.20_summits.bed INFO @ Fri, 26 Jun 2020 07:54:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (280 records, 4 fields): 2 millis CompletedMACS2peakCalling