Job ID = 6367273 SRX = SRX330985 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:20:16 prefetch.2.10.7: 1) Downloading 'SRR947190'... 2020-06-15T23:20:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:21:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:21:50 prefetch.2.10.7: 1) 'SRR947190' was downloaded successfully Read 12676608 spots for SRR947190/SRR947190.sra Written 12676608 spots for SRR947190/SRR947190.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: 00:04:13 12676608 reads; of these: 12676608 (100.00%) were unpaired; of these: 1254756 (9.90%) aligned 0 times 9329076 (73.59%) aligned exactly 1 time 2092776 (16.51%) aligned >1 times 90.10% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 7755994 / 11421852 = 0.6790 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 08:29:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.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 08:29:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:03: 1000000 INFO @ Tue, 16 Jun 2020 08:30:09: 2000000 INFO @ Tue, 16 Jun 2020 08:30:16: 3000000 INFO @ Tue, 16 Jun 2020 08:30:20: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:30:20: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:30:20: #1 total tags in treatment: 3665858 INFO @ Tue, 16 Jun 2020 08:30:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:20: #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 08:30:20: #1 tags after filtering in treatment: 3665858 INFO @ Tue, 16 Jun 2020 08:30:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:20: #2 number of paired peaks: 1210 INFO @ Tue, 16 Jun 2020 08:30:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:21: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 08:30:21: #2 alternative fragment length(s) may be 117 bps INFO @ Tue, 16 Jun 2020 08:30:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.05_model.r WARNING @ Tue, 16 Jun 2020 08:30:21: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:30:21: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Tue, 16 Jun 2020 08:30:21: #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 08:30:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:21: #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 08:30:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.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 08:30:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:32: 1000000 INFO @ Tue, 16 Jun 2020 08:30:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.05_summits.bed INFO @ Tue, 16 Jun 2020 08:30:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2124 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:30:39: 2000000 INFO @ Tue, 16 Jun 2020 08:30:46: 3000000 INFO @ Tue, 16 Jun 2020 08:30:51: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:30:51: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:30:51: #1 total tags in treatment: 3665858 INFO @ Tue, 16 Jun 2020 08:30:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:51: #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 08:30:51: #1 tags after filtering in treatment: 3665858 INFO @ Tue, 16 Jun 2020 08:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:51: #2 number of paired peaks: 1210 INFO @ Tue, 16 Jun 2020 08:30:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:51: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 08:30:51: #2 alternative fragment length(s) may be 117 bps INFO @ Tue, 16 Jun 2020 08:30:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.10_model.r WARNING @ Tue, 16 Jun 2020 08:30:51: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:30:51: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Tue, 16 Jun 2020 08:30:51: #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 08:30:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:51: #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 08:30:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.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 08:30:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:02: 1000000 INFO @ Tue, 16 Jun 2020 08:31:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.10_summits.bed INFO @ Tue, 16 Jun 2020 08:31:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1451 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:08: 2000000 INFO @ Tue, 16 Jun 2020 08:31:14: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:31:18: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:31:18: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:31:18: #1 total tags in treatment: 3665858 INFO @ Tue, 16 Jun 2020 08:31:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:18: #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 08:31:18: #1 tags after filtering in treatment: 3665858 INFO @ Tue, 16 Jun 2020 08:31:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:18: #2 number of paired peaks: 1210 INFO @ Tue, 16 Jun 2020 08:31:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:18: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 08:31:18: #2 alternative fragment length(s) may be 117 bps INFO @ Tue, 16 Jun 2020 08:31:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.20_model.r WARNING @ Tue, 16 Jun 2020 08:31:18: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:18: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Tue, 16 Jun 2020 08:31:18: #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 08:31:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:31:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX330985/SRX330985.20_summits.bed INFO @ Tue, 16 Jun 2020 08:31:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (884 records, 4 fields): 2 millis CompletedMACS2peakCalling