Job ID = 6367976 SRX = SRX4626828 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:50:03 prefetch.2.10.7: 1) Downloading 'SRR7771411'... 2020-06-15T23:50:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:37 prefetch.2.10.7: 'SRR7771411' is valid 2020-06-15T23:51:37 prefetch.2.10.7: 1) 'SRR7771411' was downloaded successfully Read 13643898 spots for SRR7771411/SRR7771411.sra Written 13643898 spots for SRR7771411/SRR7771411.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: 00:02:26 13643898 reads; of these: 13643898 (100.00%) were unpaired; of these: 1180922 (8.66%) aligned 0 times 10406196 (76.27%) aligned exactly 1 time 2056780 (15.07%) aligned >1 times 91.34% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 7968665 / 12462976 = 0.6394 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 08:57:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.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 08:57:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:57:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:57:12: 1000000 INFO @ Tue, 16 Jun 2020 08:57:17: 2000000 INFO @ Tue, 16 Jun 2020 08:57:22: 3000000 INFO @ Tue, 16 Jun 2020 08:57:27: 4000000 INFO @ Tue, 16 Jun 2020 08:57:29: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:57:29: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:57:29: #1 total tags in treatment: 4494311 INFO @ Tue, 16 Jun 2020 08:57:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:29: #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 08:57:29: #1 tags after filtering in treatment: 4494311 INFO @ Tue, 16 Jun 2020 08:57:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:30: #2 number of paired peaks: 730 WARNING @ Tue, 16 Jun 2020 08:57:30: Fewer paired peaks (730) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 730 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:30: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:57:30: #2 alternative fragment length(s) may be 3,38,513,582 bps INFO @ Tue, 16 Jun 2020 08:57:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.05_model.r WARNING @ Tue, 16 Jun 2020 08:57:30: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:57:30: #2 You may need to consider one of the other alternative d(s): 3,38,513,582 WARNING @ Tue, 16 Jun 2020 08:57:30: #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 08:57:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:30: #3 Pre-compute pvalue-qvalue table... 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 08:57:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.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 08:57:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:57:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:57:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:42: 1000000 INFO @ Tue, 16 Jun 2020 08:57:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.05_summits.bed INFO @ Tue, 16 Jun 2020 08:57:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (891 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:57:47: 2000000 INFO @ Tue, 16 Jun 2020 08:57:52: 3000000 INFO @ Tue, 16 Jun 2020 08:57:57: 4000000 INFO @ Tue, 16 Jun 2020 08:58:00: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:58:00: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:58:00: #1 total tags in treatment: 4494311 INFO @ Tue, 16 Jun 2020 08:58:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:00: #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 08:58:00: #1 tags after filtering in treatment: 4494311 INFO @ Tue, 16 Jun 2020 08:58:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:58:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:00: #2 number of paired peaks: 730 WARNING @ Tue, 16 Jun 2020 08:58:00: Fewer paired peaks (730) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 730 pairs to build model! INFO @ Tue, 16 Jun 2020 08:58:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:00: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:58:00: #2 alternative fragment length(s) may be 3,38,513,582 bps INFO @ Tue, 16 Jun 2020 08:58:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.10_model.r WARNING @ Tue, 16 Jun 2020 08:58:00: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:58:00: #2 You may need to consider one of the other alternative d(s): 3,38,513,582 WARNING @ Tue, 16 Jun 2020 08:58:00: #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 08:58:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:00: #3 Pre-compute pvalue-qvalue table... 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 08:58:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.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 08:58:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:13: 1000000 INFO @ Tue, 16 Jun 2020 08:58:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.10_summits.bed INFO @ Tue, 16 Jun 2020 08:58:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (483 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:18: 2000000 INFO @ Tue, 16 Jun 2020 08:58:24: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:58:30: 4000000 INFO @ Tue, 16 Jun 2020 08:58:32: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:58:32: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:58:32: #1 total tags in treatment: 4494311 INFO @ Tue, 16 Jun 2020 08:58:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:32: #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 08:58:33: #1 tags after filtering in treatment: 4494311 INFO @ Tue, 16 Jun 2020 08:58:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:58:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:33: #2 number of paired peaks: 730 WARNING @ Tue, 16 Jun 2020 08:58:33: Fewer paired peaks (730) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 730 pairs to build model! INFO @ Tue, 16 Jun 2020 08:58:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:33: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 08:58:33: #2 alternative fragment length(s) may be 3,38,513,582 bps INFO @ Tue, 16 Jun 2020 08:58:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.20_model.r WARNING @ Tue, 16 Jun 2020 08:58:33: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:58:33: #2 You may need to consider one of the other alternative d(s): 3,38,513,582 WARNING @ Tue, 16 Jun 2020 08:58:33: #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 08:58:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:58:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4626828/SRX4626828.20_summits.bed INFO @ Tue, 16 Jun 2020 08:58:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (158 records, 4 fields): 2 millis CompletedMACS2peakCalling