Job ID = 6367676 SRX = SRX3862415 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:32:35 prefetch.2.10.7: 1) Downloading 'SRR6914652'... 2020-06-15T23:32:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:36:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:36:06 prefetch.2.10.7: 1) 'SRR6914652' was downloaded successfully 2020-06-15T23:36:06 prefetch.2.10.7: 'SRR6914652' has 0 unresolved dependencies Read 20642661 spots for SRR6914652/SRR6914652.sra Written 20642661 spots for SRR6914652/SRR6914652.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: 00:05:39 20642661 reads; of these: 20642661 (100.00%) were unpaired; of these: 6861699 (33.24%) aligned 0 times 11588273 (56.14%) aligned exactly 1 time 2192689 (10.62%) aligned >1 times 66.76% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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_sort_core] merging from 8 files... [bam_rmdupse_core] 12526683 / 13780962 = 0.9090 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 08:45:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.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 08:45:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:45:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:49: 1000000 INFO @ Tue, 16 Jun 2020 08:45:51: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:45:51: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:45:51: #1 total tags in treatment: 1254279 INFO @ Tue, 16 Jun 2020 08:45:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:51: #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 08:45:51: #1 tags after filtering in treatment: 1254279 INFO @ Tue, 16 Jun 2020 08:45:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:51: #2 number of paired peaks: 1173 INFO @ Tue, 16 Jun 2020 08:45:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:51: #2 predicted fragment length is 68 bps INFO @ Tue, 16 Jun 2020 08:45:51: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 16 Jun 2020 08:45:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.05_model.r WARNING @ Tue, 16 Jun 2020 08:45:51: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:51: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 16 Jun 2020 08:45:51: #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 08:45:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.05_summits.bed INFO @ Tue, 16 Jun 2020 08:45:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (624 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 08:46:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.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 08:46:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:46:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:46:19: 1000000 INFO @ Tue, 16 Jun 2020 08:46:21: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:46:21: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:46:21: #1 total tags in treatment: 1254279 INFO @ Tue, 16 Jun 2020 08:46:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:46:21: #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 08:46:21: #1 tags after filtering in treatment: 1254279 INFO @ Tue, 16 Jun 2020 08:46:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:46:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:46:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:46:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:21: #2 number of paired peaks: 1173 INFO @ Tue, 16 Jun 2020 08:46:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:21: #2 predicted fragment length is 68 bps INFO @ Tue, 16 Jun 2020 08:46:21: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 16 Jun 2020 08:46:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.10_model.r WARNING @ Tue, 16 Jun 2020 08:46:21: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:46:21: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 16 Jun 2020 08:46:21: #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 08:46:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:46:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.10_summits.bed INFO @ Tue, 16 Jun 2020 08:46:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (385 records, 4 fields): 2 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 INFO @ Tue, 16 Jun 2020 08:46:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.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 08:46:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:46:41: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:46:49: 1000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:46:51: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:46:51: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:46:51: #1 total tags in treatment: 1254279 INFO @ Tue, 16 Jun 2020 08:46:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:46:51: #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 08:46:51: #1 tags after filtering in treatment: 1254279 INFO @ Tue, 16 Jun 2020 08:46:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:46:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:46:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:51: #2 number of paired peaks: 1173 INFO @ Tue, 16 Jun 2020 08:46:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:51: #2 predicted fragment length is 68 bps INFO @ Tue, 16 Jun 2020 08:46:51: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 16 Jun 2020 08:46:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.20_model.r WARNING @ Tue, 16 Jun 2020 08:46:51: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:46:51: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 16 Jun 2020 08:46:51: #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 08:46:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:46:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862415/SRX3862415.20_summits.bed INFO @ Tue, 16 Jun 2020 08:46:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (187 records, 4 fields): 6 millis CompletedMACS2peakCalling