Job ID = 10166034 SRX = SRX8832107 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:03:33 17053745 reads; of these: 17053745 (100.00%) were unpaired; of these: 2145630 (12.58%) aligned 0 times 12294007 (72.09%) aligned exactly 1 time 2614108 (15.33%) aligned >1 times 87.42% overall alignment rate Time searching: 00:03:33 Overall time: 00:03:33 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] 6096849 / 14908115 = 0.4090 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 @ Thu, 08 Oct 2020 20:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.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 @ Thu, 08 Oct 2020 20:33:06: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:33:06: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:33:11: 1000000 INFO @ Thu, 08 Oct 2020 20:33:15: 2000000 INFO @ Thu, 08 Oct 2020 20:33:20: 3000000 INFO @ Thu, 08 Oct 2020 20:33:25: 4000000 INFO @ Thu, 08 Oct 2020 20:33:30: 5000000 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 @ Thu, 08 Oct 2020 20:33:34: 6000000 INFO @ Thu, 08 Oct 2020 20:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.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 @ Thu, 08 Oct 2020 20:33:36: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:33:36: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:33:39: 7000000 INFO @ Thu, 08 Oct 2020 20:33:41: 1000000 INFO @ Thu, 08 Oct 2020 20:33:44: 8000000 INFO @ Thu, 08 Oct 2020 20:33:46: 2000000 INFO @ Thu, 08 Oct 2020 20:33:48: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 20:33:48: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 20:33:48: #1 total tags in treatment: 8811266 INFO @ Thu, 08 Oct 2020 20:33:48: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:33:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:33:49: #1 tags after filtering in treatment: 8811266 INFO @ Thu, 08 Oct 2020 20:33:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:33:49: #1 finished! INFO @ Thu, 08 Oct 2020 20:33:49: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:33:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:33:49: #2 number of paired peaks: 3501 INFO @ Thu, 08 Oct 2020 20:33:49: start model_add_line... INFO @ Thu, 08 Oct 2020 20:33:49: start X-correlation... INFO @ Thu, 08 Oct 2020 20:33:49: end of X-cor INFO @ Thu, 08 Oct 2020 20:33:49: #2 finished! INFO @ Thu, 08 Oct 2020 20:33:49: #2 predicted fragment length is 131 bps INFO @ Thu, 08 Oct 2020 20:33:49: #2 alternative fragment length(s) may be 131 bps INFO @ Thu, 08 Oct 2020 20:33:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.05_model.r INFO @ Thu, 08 Oct 2020 20:33:49: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:33:51: 3000000 INFO @ Thu, 08 Oct 2020 20:33:56: 4000000 INFO @ Thu, 08 Oct 2020 20:34:01: 5000000 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 @ Thu, 08 Oct 2020 20:34:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.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 @ Thu, 08 Oct 2020 20:34:06: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:34:06: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:34:06: 6000000 INFO @ Thu, 08 Oct 2020 20:34:10: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:34:11: 1000000 INFO @ Thu, 08 Oct 2020 20:34:11: 7000000 INFO @ Thu, 08 Oct 2020 20:34:16: 8000000 INFO @ Thu, 08 Oct 2020 20:34:16: 2000000 INFO @ Thu, 08 Oct 2020 20:34:20: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 20:34:20: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 20:34:20: #1 total tags in treatment: 8811266 INFO @ Thu, 08 Oct 2020 20:34:20: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:34:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:34:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:34:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:34:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.05_summits.bed INFO @ Thu, 08 Oct 2020 20:34:20: #1 tags after filtering in treatment: 8811266 INFO @ Thu, 08 Oct 2020 20:34:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:34:20: #1 finished! INFO @ Thu, 08 Oct 2020 20:34:20: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:34:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:34:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (9219 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:34:21: #2 number of paired peaks: 3501 INFO @ Thu, 08 Oct 2020 20:34:21: start model_add_line... INFO @ Thu, 08 Oct 2020 20:34:21: 3000000 INFO @ Thu, 08 Oct 2020 20:34:21: start X-correlation... INFO @ Thu, 08 Oct 2020 20:34:21: end of X-cor INFO @ Thu, 08 Oct 2020 20:34:21: #2 finished! INFO @ Thu, 08 Oct 2020 20:34:21: #2 predicted fragment length is 131 bps INFO @ Thu, 08 Oct 2020 20:34:21: #2 alternative fragment length(s) may be 131 bps INFO @ Thu, 08 Oct 2020 20:34:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.10_model.r INFO @ Thu, 08 Oct 2020 20:34:21: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:34:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:34:26: 4000000 INFO @ Thu, 08 Oct 2020 20:34:31: 5000000 INFO @ Thu, 08 Oct 2020 20:34:36: 6000000 INFO @ Thu, 08 Oct 2020 20:34:41: 7000000 INFO @ Thu, 08 Oct 2020 20:34:43: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:34:46: 8000000 INFO @ Thu, 08 Oct 2020 20:34:50: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 20:34:50: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 20:34:50: #1 total tags in treatment: 8811266 INFO @ Thu, 08 Oct 2020 20:34:50: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:34:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:34:50: #1 tags after filtering in treatment: 8811266 INFO @ Thu, 08 Oct 2020 20:34:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:34:50: #1 finished! INFO @ Thu, 08 Oct 2020 20:34:50: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:34:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:34:51: #2 number of paired peaks: 3501 INFO @ Thu, 08 Oct 2020 20:34:51: start model_add_line... INFO @ Thu, 08 Oct 2020 20:34:51: start X-correlation... INFO @ Thu, 08 Oct 2020 20:34:51: end of X-cor INFO @ Thu, 08 Oct 2020 20:34:51: #2 finished! INFO @ Thu, 08 Oct 2020 20:34:51: #2 predicted fragment length is 131 bps INFO @ Thu, 08 Oct 2020 20:34:51: #2 alternative fragment length(s) may be 131 bps INFO @ Thu, 08 Oct 2020 20:34:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.20_model.r INFO @ Thu, 08 Oct 2020 20:34:51: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:34:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:34:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:34:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:34:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.10_summits.bed INFO @ Thu, 08 Oct 2020 20:34:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7260 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:35:12: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:35:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:35:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:35:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832107/SRX8832107.20_summits.bed INFO @ Thu, 08 Oct 2020 20:35:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5409 records, 4 fields): 7 millis CompletedMACS2peakCalling