Job ID = 6366162 SRX = SRX065687 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:52:33 prefetch.2.10.7: 1) Downloading 'SRR217393'... 2020-06-15T23:52:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:53:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:53:01 prefetch.2.10.7: 'SRR217393' is valid 2020-06-15T23:53:01 prefetch.2.10.7: 1) 'SRR217393' was downloaded successfully Read 4445819 spots for SRR217393/SRR217393.sra Written 4445819 spots for SRR217393/SRR217393.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: 00:00:39 4445819 reads; of these: 4445819 (100.00%) were unpaired; of these: 93395 (2.10%) aligned 0 times 3693269 (83.07%) aligned exactly 1 time 659155 (14.83%) aligned >1 times 97.90% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 345521 / 4352424 = 0.0794 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 08:55:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.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 08:55:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:28: 1000000 INFO @ Tue, 16 Jun 2020 08:55:33: 2000000 INFO @ Tue, 16 Jun 2020 08:55:37: 3000000 INFO @ Tue, 16 Jun 2020 08:55:42: 4000000 INFO @ Tue, 16 Jun 2020 08:55:42: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:55:42: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:55:42: #1 total tags in treatment: 4006903 INFO @ Tue, 16 Jun 2020 08:55:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:42: #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 08:55:42: #1 tags after filtering in treatment: 4006903 INFO @ Tue, 16 Jun 2020 08:55:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:55:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:42: #2 number of paired peaks: 354 WARNING @ Tue, 16 Jun 2020 08:55:42: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Tue, 16 Jun 2020 08:55:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:42: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:55:42: #2 alternative fragment length(s) may be 4,32,585,596 bps INFO @ Tue, 16 Jun 2020 08:55:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.05_model.r WARNING @ Tue, 16 Jun 2020 08:55:42: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:55:42: #2 You may need to consider one of the other alternative d(s): 4,32,585,596 WARNING @ Tue, 16 Jun 2020 08:55:42: #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 08:55:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:50: #3 Call peaks for each chromosome... 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 08:55:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.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 08:55:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:55:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:55:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.05_summits.bed INFO @ Tue, 16 Jun 2020 08:55:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (324 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:55:58: 1000000 INFO @ Tue, 16 Jun 2020 08:56:03: 2000000 INFO @ Tue, 16 Jun 2020 08:56:08: 3000000 INFO @ Tue, 16 Jun 2020 08:56:12: 4000000 INFO @ Tue, 16 Jun 2020 08:56:12: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:56:12: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:56:12: #1 total tags in treatment: 4006903 INFO @ Tue, 16 Jun 2020 08:56:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:12: #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 08:56:12: #1 tags after filtering in treatment: 4006903 INFO @ Tue, 16 Jun 2020 08:56:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:13: #2 number of paired peaks: 354 WARNING @ Tue, 16 Jun 2020 08:56:13: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Tue, 16 Jun 2020 08:56:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:13: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:56:13: #2 alternative fragment length(s) may be 4,32,585,596 bps INFO @ Tue, 16 Jun 2020 08:56:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.10_model.r WARNING @ Tue, 16 Jun 2020 08:56:13: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:56:13: #2 You may need to consider one of the other alternative d(s): 4,32,585,596 WARNING @ Tue, 16 Jun 2020 08:56:13: #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 08:56:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:20: #3 Call peaks for each chromosome... 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 08:56:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.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 08:56:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.10_summits.bed INFO @ Tue, 16 Jun 2020 08:56:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:56:28: 1000000 INFO @ Tue, 16 Jun 2020 08:56:33: 2000000 INFO @ Tue, 16 Jun 2020 08:56:38: 3000000 INFO @ Tue, 16 Jun 2020 08:56:42: 4000000 INFO @ Tue, 16 Jun 2020 08:56:42: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:56:42: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:56:42: #1 total tags in treatment: 4006903 INFO @ Tue, 16 Jun 2020 08:56:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:42: #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 08:56:42: #1 tags after filtering in treatment: 4006903 INFO @ Tue, 16 Jun 2020 08:56:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:42: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:56:43: #2 number of paired peaks: 354 WARNING @ Tue, 16 Jun 2020 08:56:43: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Tue, 16 Jun 2020 08:56:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:43: #2 predicted fragment length is 32 bps INFO @ Tue, 16 Jun 2020 08:56:43: #2 alternative fragment length(s) may be 4,32,585,596 bps INFO @ Tue, 16 Jun 2020 08:56:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.20_model.r WARNING @ Tue, 16 Jun 2020 08:56:43: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:56:43: #2 You may need to consider one of the other alternative d(s): 4,32,585,596 WARNING @ Tue, 16 Jun 2020 08:56:43: #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 08:56:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:56:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:56:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:56:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065687/SRX065687.20_summits.bed INFO @ Tue, 16 Jun 2020 08:56:55: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (40 records, 4 fields): 1 millis CompletedMACS2peakCalling