Job ID = 6507970 SRX = SRX514570 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:33:17 prefetch.2.10.7: 1) Downloading 'SRR1230858'... 2020-06-26T13:33:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:34:10 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:34:11 prefetch.2.10.7: 'SRR1230858' is valid 2020-06-26T13:34:11 prefetch.2.10.7: 1) 'SRR1230858' was downloaded successfully Read 4995351 spots for SRR1230858/SRR1230858.sra Written 4995351 spots for SRR1230858/SRR1230858.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: 00:01:15 4995351 reads; of these: 4995351 (100.00%) were unpaired; of these: 704352 (14.10%) aligned 0 times 3563495 (71.34%) aligned exactly 1 time 727504 (14.56%) aligned >1 times 85.90% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:16 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] 264888 / 4290999 = 0.0617 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 22:37:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.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 22:37:27: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:27: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:35: 1000000 INFO @ Fri, 26 Jun 2020 22:37:42: 2000000 INFO @ Fri, 26 Jun 2020 22:37:50: 3000000 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 22:37:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.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 22:37:54: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:54: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:58: 4000000 INFO @ Fri, 26 Jun 2020 22:37:58: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:37:58: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:37:58: #1 total tags in treatment: 4026111 INFO @ Fri, 26 Jun 2020 22:37:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:37:58: #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 22:37:58: #1 tags after filtering in treatment: 4026111 INFO @ Fri, 26 Jun 2020 22:37:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:37:58: #1 finished! INFO @ Fri, 26 Jun 2020 22:37:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:37:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:37:58: #2 number of paired peaks: 381 WARNING @ Fri, 26 Jun 2020 22:37:58: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 26 Jun 2020 22:37:58: start model_add_line... INFO @ Fri, 26 Jun 2020 22:37:58: start X-correlation... INFO @ Fri, 26 Jun 2020 22:37:58: end of X-cor INFO @ Fri, 26 Jun 2020 22:37:58: #2 finished! INFO @ Fri, 26 Jun 2020 22:37:58: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 22:37:58: #2 alternative fragment length(s) may be 49,508 bps INFO @ Fri, 26 Jun 2020 22:37:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.05_model.r WARNING @ Fri, 26 Jun 2020 22:37:58: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:37:58: #2 You may need to consider one of the other alternative d(s): 49,508 WARNING @ Fri, 26 Jun 2020 22:37:58: #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 22:37:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:37:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:38:02: 1000000 INFO @ Fri, 26 Jun 2020 22:38:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:38:10: 2000000 INFO @ Fri, 26 Jun 2020 22:38:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:38:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:38:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.05_summits.bed INFO @ Fri, 26 Jun 2020 22:38:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (462 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:38:17: 3000000 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 22:38:24: 4000000 INFO @ Fri, 26 Jun 2020 22:38:24: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:38:24: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:38:24: #1 total tags in treatment: 4026111 INFO @ Fri, 26 Jun 2020 22:38:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:38:24: #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 22:38:24: #1 tags after filtering in treatment: 4026111 INFO @ Fri, 26 Jun 2020 22:38:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:38:24: #1 finished! INFO @ Fri, 26 Jun 2020 22:38:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:38:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:38:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.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 22:38:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:38:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:38:24: #2 number of paired peaks: 381 WARNING @ Fri, 26 Jun 2020 22:38:24: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 26 Jun 2020 22:38:24: start model_add_line... INFO @ Fri, 26 Jun 2020 22:38:24: start X-correlation... INFO @ Fri, 26 Jun 2020 22:38:24: end of X-cor INFO @ Fri, 26 Jun 2020 22:38:24: #2 finished! INFO @ Fri, 26 Jun 2020 22:38:24: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 22:38:24: #2 alternative fragment length(s) may be 49,508 bps INFO @ Fri, 26 Jun 2020 22:38:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.10_model.r WARNING @ Fri, 26 Jun 2020 22:38:24: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:38:24: #2 You may need to consider one of the other alternative d(s): 49,508 WARNING @ Fri, 26 Jun 2020 22:38:24: #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 22:38:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:38:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:38:32: 1000000 INFO @ Fri, 26 Jun 2020 22:38:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:38:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:38:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:38:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.10_summits.bed INFO @ Fri, 26 Jun 2020 22:38:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (248 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:38:39: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:38:47: 3000000 INFO @ Fri, 26 Jun 2020 22:38:54: 4000000 INFO @ Fri, 26 Jun 2020 22:38:54: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:38:54: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:38:54: #1 total tags in treatment: 4026111 INFO @ Fri, 26 Jun 2020 22:38:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:38:54: #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 22:38:54: #1 tags after filtering in treatment: 4026111 INFO @ Fri, 26 Jun 2020 22:38:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:38:54: #1 finished! INFO @ Fri, 26 Jun 2020 22:38:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:38:54: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:38:55: #2 number of paired peaks: 381 WARNING @ Fri, 26 Jun 2020 22:38:55: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Fri, 26 Jun 2020 22:38:55: start model_add_line... INFO @ Fri, 26 Jun 2020 22:38:55: start X-correlation... INFO @ Fri, 26 Jun 2020 22:38:55: end of X-cor INFO @ Fri, 26 Jun 2020 22:38:55: #2 finished! INFO @ Fri, 26 Jun 2020 22:38:55: #2 predicted fragment length is 49 bps INFO @ Fri, 26 Jun 2020 22:38:55: #2 alternative fragment length(s) may be 49,508 bps INFO @ Fri, 26 Jun 2020 22:38:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.20_model.r WARNING @ Fri, 26 Jun 2020 22:38:55: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:38:55: #2 You may need to consider one of the other alternative d(s): 49,508 WARNING @ Fri, 26 Jun 2020 22:38:55: #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 22:38:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:38:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:39:04: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:39:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:39:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:39:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX514570/SRX514570.20_summits.bed INFO @ Fri, 26 Jun 2020 22:39:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (107 records, 4 fields): 2 millis CompletedMACS2peakCalling