Job ID = 10166044 SRX = SRX8832110 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: 00:03:18 19166326 reads; of these: 19166326 (100.00%) were unpaired; of these: 5385994 (28.10%) aligned 0 times 11290385 (58.91%) aligned exactly 1 time 2489947 (12.99%) aligned >1 times 71.90% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 5018154 / 13780332 = 0.3642 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 20:34:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.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 20:34:25: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:34:25: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:34:29: 1000000 INFO @ Thu, 08 Oct 2020 20:34:34: 2000000 INFO @ Thu, 08 Oct 2020 20:34:38: 3000000 INFO @ Thu, 08 Oct 2020 20:34:43: 4000000 INFO @ Thu, 08 Oct 2020 20:34:48: 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 20:34:52: 6000000 INFO @ Thu, 08 Oct 2020 20:34:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.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 20:34:54: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:34:54: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:34:57: 7000000 INFO @ Thu, 08 Oct 2020 20:34:59: 1000000 INFO @ Thu, 08 Oct 2020 20:35:01: 8000000 INFO @ Thu, 08 Oct 2020 20:35:04: 2000000 INFO @ Thu, 08 Oct 2020 20:35:05: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:35:05: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:35:05: #1 total tags in treatment: 8762178 INFO @ Thu, 08 Oct 2020 20:35:05: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:35:05: #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 20:35:05: #1 tags after filtering in treatment: 8762178 INFO @ Thu, 08 Oct 2020 20:35:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:35:05: #1 finished! INFO @ Thu, 08 Oct 2020 20:35:05: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:35:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:35:06: #2 number of paired peaks: 4998 INFO @ Thu, 08 Oct 2020 20:35:06: start model_add_line... INFO @ Thu, 08 Oct 2020 20:35:06: start X-correlation... INFO @ Thu, 08 Oct 2020 20:35:06: end of X-cor INFO @ Thu, 08 Oct 2020 20:35:06: #2 finished! INFO @ Thu, 08 Oct 2020 20:35:06: #2 predicted fragment length is 160 bps INFO @ Thu, 08 Oct 2020 20:35:06: #2 alternative fragment length(s) may be 160 bps INFO @ Thu, 08 Oct 2020 20:35:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.05_model.r INFO @ Thu, 08 Oct 2020 20:35:06: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:35:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:35:08: 3000000 INFO @ Thu, 08 Oct 2020 20:35:13: 4000000 INFO @ Thu, 08 Oct 2020 20:35:17: 5000000 INFO @ Thu, 08 Oct 2020 20:35:22: 6000000 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 20:35:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.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 20:35:26: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:35:26: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:35:26: 7000000 INFO @ Thu, 08 Oct 2020 20:35:30: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:35:31: 1000000 INFO @ Thu, 08 Oct 2020 20:35:31: 8000000 INFO @ Thu, 08 Oct 2020 20:35:35: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:35:35: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:35:35: #1 total tags in treatment: 8762178 INFO @ Thu, 08 Oct 2020 20:35:35: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:35:35: #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 20:35:35: #1 tags after filtering in treatment: 8762178 INFO @ Thu, 08 Oct 2020 20:35:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:35:35: #1 finished! INFO @ Thu, 08 Oct 2020 20:35:35: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:35:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:35:36: 2000000 INFO @ Thu, 08 Oct 2020 20:35:36: #2 number of paired peaks: 4998 INFO @ Thu, 08 Oct 2020 20:35:36: start model_add_line... INFO @ Thu, 08 Oct 2020 20:35:36: start X-correlation... INFO @ Thu, 08 Oct 2020 20:35:36: end of X-cor INFO @ Thu, 08 Oct 2020 20:35:36: #2 finished! INFO @ Thu, 08 Oct 2020 20:35:36: #2 predicted fragment length is 160 bps INFO @ Thu, 08 Oct 2020 20:35:36: #2 alternative fragment length(s) may be 160 bps INFO @ Thu, 08 Oct 2020 20:35:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.10_model.r INFO @ Thu, 08 Oct 2020 20:35:36: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:35:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:35:40: 3000000 INFO @ Thu, 08 Oct 2020 20:35:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:35:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:35:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.05_summits.bed INFO @ Thu, 08 Oct 2020 20:35:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (9972 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:35:45: 4000000 INFO @ Thu, 08 Oct 2020 20:35:50: 5000000 INFO @ Thu, 08 Oct 2020 20:35:55: 6000000 INFO @ Thu, 08 Oct 2020 20:36:00: 7000000 INFO @ Thu, 08 Oct 2020 20:36:00: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:36:04: 8000000 INFO @ Thu, 08 Oct 2020 20:36:08: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:36:08: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:36:08: #1 total tags in treatment: 8762178 INFO @ Thu, 08 Oct 2020 20:36:08: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:36:08: #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 20:36:08: #1 tags after filtering in treatment: 8762178 INFO @ Thu, 08 Oct 2020 20:36:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:36:08: #1 finished! INFO @ Thu, 08 Oct 2020 20:36:08: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:36:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:36:09: #2 number of paired peaks: 4998 INFO @ Thu, 08 Oct 2020 20:36:09: start model_add_line... INFO @ Thu, 08 Oct 2020 20:36:09: start X-correlation... INFO @ Thu, 08 Oct 2020 20:36:09: end of X-cor INFO @ Thu, 08 Oct 2020 20:36:09: #2 finished! INFO @ Thu, 08 Oct 2020 20:36:09: #2 predicted fragment length is 160 bps INFO @ Thu, 08 Oct 2020 20:36:09: #2 alternative fragment length(s) may be 160 bps INFO @ Thu, 08 Oct 2020 20:36:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.20_model.r INFO @ Thu, 08 Oct 2020 20:36:09: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:36:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:36:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:36:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:36:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.10_summits.bed INFO @ Thu, 08 Oct 2020 20:36:12: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8120 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:36:34: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:36:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:36:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:36:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832110/SRX8832110.20_summits.bed INFO @ Thu, 08 Oct 2020 20:36:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6173 records, 4 fields): 25 millis CompletedMACS2peakCalling