Job ID = 6367978 SRX = SRX4626830 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:40:14 prefetch.2.10.7: 1) Downloading 'SRR7771413'... 2020-06-15T23:40:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:54 prefetch.2.10.7: 'SRR7771413' is valid 2020-06-15T23:42:54 prefetch.2.10.7: 1) 'SRR7771413' was downloaded successfully Read 13892491 spots for SRR7771413/SRR7771413.sra Written 13892491 spots for SRR7771413/SRR7771413.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: 00:00:00 Multiseed full-index search: 00:02:24 13892491 reads; of these: 13892491 (100.00%) were unpaired; of these: 828240 (5.96%) aligned 0 times 10986799 (79.08%) aligned exactly 1 time 2077452 (14.95%) aligned >1 times 94.04% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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] 7561942 / 13064251 = 0.5788 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 08:48:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.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 08:48:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:36: 1000000 INFO @ Tue, 16 Jun 2020 08:48:42: 2000000 INFO @ Tue, 16 Jun 2020 08:48:47: 3000000 INFO @ Tue, 16 Jun 2020 08:48:53: 4000000 INFO @ Tue, 16 Jun 2020 08:48:58: 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 @ Tue, 16 Jun 2020 08:49:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.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 08:49:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:01: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:49:01: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:49:01: #1 total tags in treatment: 5502309 INFO @ Tue, 16 Jun 2020 08:49:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:01: #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 08:49:01: #1 tags after filtering in treatment: 5502309 INFO @ Tue, 16 Jun 2020 08:49:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:02: #2 number of paired peaks: 666 WARNING @ Tue, 16 Jun 2020 08:49:02: Fewer paired peaks (666) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 666 pairs to build model! INFO @ Tue, 16 Jun 2020 08:49:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:02: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 08:49:02: #2 alternative fragment length(s) may be 4,43 bps INFO @ Tue, 16 Jun 2020 08:49:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.05_model.r WARNING @ Tue, 16 Jun 2020 08:49:02: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:49:02: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Tue, 16 Jun 2020 08:49:02: #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 08:49:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:07: 1000000 INFO @ Tue, 16 Jun 2020 08:49:12: 2000000 INFO @ Tue, 16 Jun 2020 08:49:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:18: 3000000 INFO @ Tue, 16 Jun 2020 08:49:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.05_summits.bed INFO @ Tue, 16 Jun 2020 08:49:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1168 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:49:24: 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 08:49:30: 5000000 INFO @ Tue, 16 Jun 2020 08:49:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.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 08:49:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:33: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:49:33: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:49:33: #1 total tags in treatment: 5502309 INFO @ Tue, 16 Jun 2020 08:49:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:33: #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 08:49:33: #1 tags after filtering in treatment: 5502309 INFO @ Tue, 16 Jun 2020 08:49:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:33: #2 number of paired peaks: 666 WARNING @ Tue, 16 Jun 2020 08:49:33: Fewer paired peaks (666) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 666 pairs to build model! INFO @ Tue, 16 Jun 2020 08:49:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:33: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 08:49:33: #2 alternative fragment length(s) may be 4,43 bps INFO @ Tue, 16 Jun 2020 08:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.10_model.r WARNING @ Tue, 16 Jun 2020 08:49:33: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:49:33: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Tue, 16 Jun 2020 08:49:33: #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 08:49:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:36: 1000000 INFO @ Tue, 16 Jun 2020 08:49:42: 2000000 INFO @ Tue, 16 Jun 2020 08:49:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:48: 3000000 INFO @ Tue, 16 Jun 2020 08:49:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.10_summits.bed INFO @ Tue, 16 Jun 2020 08:49:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (570 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:49:54: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:50:00: 5000000 INFO @ Tue, 16 Jun 2020 08:50:03: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:50:03: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:50:03: #1 total tags in treatment: 5502309 INFO @ Tue, 16 Jun 2020 08:50:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:03: #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 08:50:03: #1 tags after filtering in treatment: 5502309 INFO @ Tue, 16 Jun 2020 08:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:04: #2 number of paired peaks: 666 WARNING @ Tue, 16 Jun 2020 08:50:04: Fewer paired peaks (666) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 666 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:04: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 08:50:04: #2 alternative fragment length(s) may be 4,43 bps INFO @ Tue, 16 Jun 2020 08:50:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.20_model.r WARNING @ Tue, 16 Jun 2020 08:50:04: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:04: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Tue, 16 Jun 2020 08:50:04: #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 08:50:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:50:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4626830/SRX4626830.20_summits.bed INFO @ Tue, 16 Jun 2020 08:50:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (185 records, 4 fields): 2 millis CompletedMACS2peakCalling