Job ID = 6368664 SRX = SRX529224 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:28:31 prefetch.2.10.7: 1) Downloading 'SRR1265828'... 2020-06-16T00:28:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:08 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:08 prefetch.2.10.7: 'SRR1265828' is valid 2020-06-16T00:30:08 prefetch.2.10.7: 1) 'SRR1265828' was downloaded successfully Read 8711649 spots for SRR1265828/SRR1265828.sra Written 8711649 spots for SRR1265828/SRR1265828.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: 00:02:05 8711649 reads; of these: 8711649 (100.00%) were unpaired; of these: 197291 (2.26%) aligned 0 times 6910231 (79.32%) aligned exactly 1 time 1604127 (18.41%) aligned >1 times 97.74% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 1241988 / 8514358 = 0.1459 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 09:35:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.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 09:35:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:18: 1000000 INFO @ Tue, 16 Jun 2020 09:35:23: 2000000 INFO @ Tue, 16 Jun 2020 09:35:29: 3000000 INFO @ Tue, 16 Jun 2020 09:35:34: 4000000 INFO @ Tue, 16 Jun 2020 09:35:39: 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 09:35:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.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 09:35:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:45: 6000000 INFO @ Tue, 16 Jun 2020 09:35:49: 1000000 INFO @ Tue, 16 Jun 2020 09:35:52: 7000000 INFO @ Tue, 16 Jun 2020 09:35:54: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:35:54: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:35:54: #1 total tags in treatment: 7272370 INFO @ Tue, 16 Jun 2020 09:35:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:54: #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 09:35:54: #1 tags after filtering in treatment: 7272370 INFO @ Tue, 16 Jun 2020 09:35:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:54: #2 number of paired peaks: 356 WARNING @ Tue, 16 Jun 2020 09:35:54: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:54: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:35:54: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 16 Jun 2020 09:35:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.05_model.r WARNING @ Tue, 16 Jun 2020 09:35:54: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:54: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 16 Jun 2020 09:35:54: #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 09:35:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:55: 2000000 INFO @ Tue, 16 Jun 2020 09:36:02: 3000000 INFO @ Tue, 16 Jun 2020 09:36:07: 4000000 INFO @ Tue, 16 Jun 2020 09:36:08: #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 09:36:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.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 09:36:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:13: 5000000 INFO @ Tue, 16 Jun 2020 09:36:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.05_summits.bed INFO @ Tue, 16 Jun 2020 09:36:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (633 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:19: 1000000 INFO @ Tue, 16 Jun 2020 09:36:20: 6000000 INFO @ Tue, 16 Jun 2020 09:36:25: 2000000 INFO @ Tue, 16 Jun 2020 09:36:26: 7000000 INFO @ Tue, 16 Jun 2020 09:36:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:36:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:36:28: #1 total tags in treatment: 7272370 INFO @ Tue, 16 Jun 2020 09:36:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:28: #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 09:36:28: #1 tags after filtering in treatment: 7272370 INFO @ Tue, 16 Jun 2020 09:36:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:28: #2 number of paired peaks: 356 WARNING @ Tue, 16 Jun 2020 09:36:28: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:28: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:36:28: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 16 Jun 2020 09:36:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.10_model.r WARNING @ Tue, 16 Jun 2020 09:36:28: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:28: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 16 Jun 2020 09:36:28: #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 09:36:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:32: 3000000 INFO @ Tue, 16 Jun 2020 09:36:38: 4000000 INFO @ Tue, 16 Jun 2020 09:36:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:44: 5000000 INFO @ Tue, 16 Jun 2020 09:36:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.10_summits.bed INFO @ Tue, 16 Jun 2020 09:36:49: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (411 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:50: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:36:56: 7000000 INFO @ Tue, 16 Jun 2020 09:36:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:36:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:36:58: #1 total tags in treatment: 7272370 INFO @ Tue, 16 Jun 2020 09:36:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:58: #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 09:36:58: #1 tags after filtering in treatment: 7272370 INFO @ Tue, 16 Jun 2020 09:36:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:58: #2 number of paired peaks: 356 WARNING @ Tue, 16 Jun 2020 09:36:58: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:59: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:36:59: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 16 Jun 2020 09:36:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.20_model.r WARNING @ Tue, 16 Jun 2020 09:36:59: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:59: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 16 Jun 2020 09:36:59: #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 09:36:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:37:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529224/SRX529224.20_summits.bed INFO @ Tue, 16 Jun 2020 09:37:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (170 records, 4 fields): 1 millis CompletedMACS2peakCalling