Job ID = 6368777 SRX = SRX560681 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:23:03 prefetch.2.10.7: 1) Downloading 'SRR1314158'... 2020-06-16T00:23:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:23:56 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:23:57 prefetch.2.10.7: 'SRR1314158' is valid 2020-06-16T00:23:57 prefetch.2.10.7: 1) 'SRR1314158' was downloaded successfully 2020-06-16T00:23:57 prefetch.2.10.7: 'SRR1314158' has 0 unresolved dependencies Read 5798539 spots for SRR1314158/SRR1314158.sra Written 5798539 spots for SRR1314158/SRR1314158.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: 00:00:49 5798539 reads; of these: 5798539 (100.00%) were unpaired; of these: 5033089 (86.80%) aligned 0 times 639728 (11.03%) aligned exactly 1 time 125722 (2.17%) aligned >1 times 13.20% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 734480 / 765450 = 0.9595 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 09:25:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.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 09:25:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:52: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:25:52: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:25:52: #1 total tags in treatment: 30970 INFO @ Tue, 16 Jun 2020 09:25:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:52: #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 09:25:52: #1 tags after filtering in treatment: 30970 INFO @ Tue, 16 Jun 2020 09:25:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:52: #2 number of paired peaks: 4387 INFO @ Tue, 16 Jun 2020 09:25:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:52: #2 predicted fragment length is 102 bps INFO @ Tue, 16 Jun 2020 09:25:52: #2 alternative fragment length(s) may be 1,102,160,222,267,298,420,492,526,587 bps INFO @ Tue, 16 Jun 2020 09:25:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.05_model.r WARNING @ Tue, 16 Jun 2020 09:25:52: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:25:52: #2 You may need to consider one of the other alternative d(s): 1,102,160,222,267,298,420,492,526,587 WARNING @ Tue, 16 Jun 2020 09:25:52: #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 09:25:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:25:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.05_summits.bed INFO @ Tue, 16 Jun 2020 09:25:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (34 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 09:26:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.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 09:26:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:22: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:26:22: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:26:22: #1 total tags in treatment: 30970 INFO @ Tue, 16 Jun 2020 09:26:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:22: #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 09:26:22: #1 tags after filtering in treatment: 30970 INFO @ Tue, 16 Jun 2020 09:26:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:22: #2 number of paired peaks: 4387 INFO @ Tue, 16 Jun 2020 09:26:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:22: #2 predicted fragment length is 102 bps INFO @ Tue, 16 Jun 2020 09:26:22: #2 alternative fragment length(s) may be 1,102,160,222,267,298,420,492,526,587 bps INFO @ Tue, 16 Jun 2020 09:26:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.10_model.r WARNING @ Tue, 16 Jun 2020 09:26:22: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:22: #2 You may need to consider one of the other alternative d(s): 1,102,160,222,267,298,420,492,526,587 WARNING @ Tue, 16 Jun 2020 09:26:22: #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 09:26:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.10_summits.bed INFO @ Tue, 16 Jun 2020 09:26:22: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:26:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.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 09:26:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:52: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:26:52: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:26:52: #1 total tags in treatment: 30970 INFO @ Tue, 16 Jun 2020 09:26:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:52: #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 09:26:52: #1 tags after filtering in treatment: 30970 INFO @ Tue, 16 Jun 2020 09:26:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:52: #2 number of paired peaks: 4387 INFO @ Tue, 16 Jun 2020 09:26:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:52: #2 predicted fragment length is 102 bps INFO @ Tue, 16 Jun 2020 09:26:52: #2 alternative fragment length(s) may be 1,102,160,222,267,298,420,492,526,587 bps INFO @ Tue, 16 Jun 2020 09:26:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.20_model.r WARNING @ Tue, 16 Jun 2020 09:26:52: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:52: #2 You may need to consider one of the other alternative d(s): 1,102,160,222,267,298,420,492,526,587 WARNING @ Tue, 16 Jun 2020 09:26:52: #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 09:26:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX560681/SRX560681.20_summits.bed INFO @ Tue, 16 Jun 2020 09:26:52: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis CompletedMACS2peakCalling