Job ID = 6368955 SRX = SRX7627595 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:41:03 prefetch.2.10.7: 1) Downloading 'SRR10961945'... 2020-06-16T00:41:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:43:12 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:43:13 prefetch.2.10.7: 'SRR10961945' is valid 2020-06-16T00:43:13 prefetch.2.10.7: 1) 'SRR10961945' was downloaded successfully Read 13642872 spots for SRR10961945/SRR10961945.sra Written 13642872 spots for SRR10961945/SRR10961945.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: 00:02:20 13642872 reads; of these: 13642872 (100.00%) were unpaired; of these: 5411929 (39.67%) aligned 0 times 6872374 (50.37%) aligned exactly 1 time 1358569 (9.96%) aligned >1 times 60.33% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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] 1387392 / 8230943 = 0.1686 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 @ Tue, 16 Jun 2020 09:48:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.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 @ Tue, 16 Jun 2020 09:48:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:51: 1000000 INFO @ Tue, 16 Jun 2020 09:48:58: 2000000 INFO @ Tue, 16 Jun 2020 09:49:04: 3000000 INFO @ Tue, 16 Jun 2020 09:49:10: 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 @ Tue, 16 Jun 2020 09:49:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.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 @ Tue, 16 Jun 2020 09:49:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:17: 5000000 INFO @ Tue, 16 Jun 2020 09:49:21: 1000000 INFO @ Tue, 16 Jun 2020 09:49:24: 6000000 INFO @ Tue, 16 Jun 2020 09:49:29: 2000000 INFO @ Tue, 16 Jun 2020 09:49:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:31: #1 total tags in treatment: 6843551 INFO @ Tue, 16 Jun 2020 09:49:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:49:31: #1 tags after filtering in treatment: 6843551 INFO @ Tue, 16 Jun 2020 09:49:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:31: #2 number of paired peaks: 365 WARNING @ Tue, 16 Jun 2020 09:49:31: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:31: #2 predicted fragment length is 59 bps INFO @ Tue, 16 Jun 2020 09:49:31: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 16 Jun 2020 09:49:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.05_model.r WARNING @ Tue, 16 Jun 2020 09:49:31: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:31: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 16 Jun 2020 09:49:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:49:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:35: 3000000 INFO @ Tue, 16 Jun 2020 09:49:42: 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 @ Tue, 16 Jun 2020 09:49:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.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 @ Tue, 16 Jun 2020 09:49:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:49: 5000000 INFO @ Tue, 16 Jun 2020 09:49:52: 1000000 INFO @ Tue, 16 Jun 2020 09:49:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.05_summits.bed INFO @ Tue, 16 Jun 2020 09:49:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (704 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:57: 6000000 INFO @ Tue, 16 Jun 2020 09:50:00: 2000000 INFO @ Tue, 16 Jun 2020 09:50:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:03: #1 total tags in treatment: 6843551 INFO @ Tue, 16 Jun 2020 09:50:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:50:04: #1 tags after filtering in treatment: 6843551 INFO @ Tue, 16 Jun 2020 09:50:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:04: #2 number of paired peaks: 365 WARNING @ Tue, 16 Jun 2020 09:50:04: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:04: #2 predicted fragment length is 59 bps INFO @ Tue, 16 Jun 2020 09:50:04: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 16 Jun 2020 09:50:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.10_model.r WARNING @ Tue, 16 Jun 2020 09:50:04: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:04: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 16 Jun 2020 09:50:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:50:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:07: 3000000 INFO @ Tue, 16 Jun 2020 09:50:14: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:50:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:21: 5000000 INFO @ Tue, 16 Jun 2020 09:50:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.10_summits.bed INFO @ Tue, 16 Jun 2020 09:50:26: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (429 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:50:28: 6000000 INFO @ Tue, 16 Jun 2020 09:50:33: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:33: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:33: #1 total tags in treatment: 6843551 INFO @ Tue, 16 Jun 2020 09:50:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:50:33: #1 tags after filtering in treatment: 6843551 INFO @ Tue, 16 Jun 2020 09:50:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:33: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:50:34: #2 number of paired peaks: 365 WARNING @ Tue, 16 Jun 2020 09:50:34: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:34: #2 predicted fragment length is 59 bps INFO @ Tue, 16 Jun 2020 09:50:34: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 16 Jun 2020 09:50:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.20_model.r WARNING @ Tue, 16 Jun 2020 09:50:34: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:34: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 16 Jun 2020 09:50:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:50:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7627595/SRX7627595.20_summits.bed INFO @ Tue, 16 Jun 2020 09:50:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (187 records, 4 fields): 1 millis CompletedMACS2peakCalling