Job ID = 14160708 SRX = SRX10399027 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: 00:04:06 13755672 reads; of these: 13755672 (100.00%) were unpaired; of these: 2548292 (18.53%) aligned 0 times 9367383 (68.10%) aligned exactly 1 time 1839997 (13.38%) aligned >1 times 81.47% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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] 1844294 / 11207380 = 0.1646 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:55:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.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, 09 Dec 2021 03:55:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:55:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:55:51: 1000000 INFO @ Thu, 09 Dec 2021 03:55:56: 2000000 INFO @ Thu, 09 Dec 2021 03:56:01: 3000000 INFO @ Thu, 09 Dec 2021 03:56:07: 4000000 INFO @ Thu, 09 Dec 2021 03:56:12: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:56:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.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, 09 Dec 2021 03:56:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:56:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:56:17: 6000000 INFO @ Thu, 09 Dec 2021 03:56:21: 1000000 INFO @ Thu, 09 Dec 2021 03:56:23: 7000000 INFO @ Thu, 09 Dec 2021 03:56:27: 2000000 INFO @ Thu, 09 Dec 2021 03:56:28: 8000000 INFO @ Thu, 09 Dec 2021 03:56:32: 3000000 INFO @ Thu, 09 Dec 2021 03:56:34: 9000000 INFO @ Thu, 09 Dec 2021 03:56:36: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:56:36: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:56:36: #1 total tags in treatment: 9363086 INFO @ Thu, 09 Dec 2021 03:56:36: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:56:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:56:36: #1 tags after filtering in treatment: 9363086 INFO @ Thu, 09 Dec 2021 03:56:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:56:36: #1 finished! INFO @ Thu, 09 Dec 2021 03:56:36: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:56:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:56:37: #2 number of paired peaks: 627 WARNING @ Thu, 09 Dec 2021 03:56:37: Fewer paired peaks (627) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 627 pairs to build model! INFO @ Thu, 09 Dec 2021 03:56:37: start model_add_line... INFO @ Thu, 09 Dec 2021 03:56:37: start X-correlation... INFO @ Thu, 09 Dec 2021 03:56:37: end of X-cor INFO @ Thu, 09 Dec 2021 03:56:37: #2 finished! INFO @ Thu, 09 Dec 2021 03:56:37: #2 predicted fragment length is 188 bps INFO @ Thu, 09 Dec 2021 03:56:37: #2 alternative fragment length(s) may be 188 bps INFO @ Thu, 09 Dec 2021 03:56:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.05_model.r INFO @ Thu, 09 Dec 2021 03:56:37: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:56:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:56:38: 4000000 INFO @ Thu, 09 Dec 2021 03:56:43: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:56:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.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, 09 Dec 2021 03:56:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:56:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:56:49: 6000000 INFO @ Thu, 09 Dec 2021 03:56:52: 1000000 INFO @ Thu, 09 Dec 2021 03:56:55: 7000000 INFO @ Thu, 09 Dec 2021 03:56:58: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:56:59: 2000000 INFO @ Thu, 09 Dec 2021 03:57:01: 8000000 INFO @ Thu, 09 Dec 2021 03:57:06: 3000000 INFO @ Thu, 09 Dec 2021 03:57:06: 9000000 INFO @ Thu, 09 Dec 2021 03:57:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:57:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:57:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.05_summits.bed INFO @ Thu, 09 Dec 2021 03:57:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1842 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:57:08: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:57:08: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:57:08: #1 total tags in treatment: 9363086 INFO @ Thu, 09 Dec 2021 03:57:08: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:57:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:57:09: #1 tags after filtering in treatment: 9363086 INFO @ Thu, 09 Dec 2021 03:57:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:57:09: #1 finished! INFO @ Thu, 09 Dec 2021 03:57:09: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:57:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:57:09: #2 number of paired peaks: 627 WARNING @ Thu, 09 Dec 2021 03:57:09: Fewer paired peaks (627) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 627 pairs to build model! INFO @ Thu, 09 Dec 2021 03:57:09: start model_add_line... INFO @ Thu, 09 Dec 2021 03:57:09: start X-correlation... INFO @ Thu, 09 Dec 2021 03:57:09: end of X-cor INFO @ Thu, 09 Dec 2021 03:57:09: #2 finished! INFO @ Thu, 09 Dec 2021 03:57:09: #2 predicted fragment length is 188 bps INFO @ Thu, 09 Dec 2021 03:57:09: #2 alternative fragment length(s) may be 188 bps INFO @ Thu, 09 Dec 2021 03:57:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.10_model.r INFO @ Thu, 09 Dec 2021 03:57:09: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:57:12: 4000000 INFO @ Thu, 09 Dec 2021 03:57:19: 5000000 INFO @ Thu, 09 Dec 2021 03:57:25: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:57:29: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:57:32: 7000000 INFO @ Thu, 09 Dec 2021 03:57:38: 8000000 INFO @ Thu, 09 Dec 2021 03:57:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:57:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:57:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.10_summits.bed INFO @ Thu, 09 Dec 2021 03:57:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1183 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:57:44: 9000000 INFO @ Thu, 09 Dec 2021 03:57:46: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:57:46: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:57:46: #1 total tags in treatment: 9363086 INFO @ Thu, 09 Dec 2021 03:57:46: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:57:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:57:47: #1 tags after filtering in treatment: 9363086 INFO @ Thu, 09 Dec 2021 03:57:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:57:47: #1 finished! INFO @ Thu, 09 Dec 2021 03:57:47: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:57:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:57:47: #2 number of paired peaks: 627 WARNING @ Thu, 09 Dec 2021 03:57:47: Fewer paired peaks (627) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 627 pairs to build model! INFO @ Thu, 09 Dec 2021 03:57:47: start model_add_line... INFO @ Thu, 09 Dec 2021 03:57:47: start X-correlation... INFO @ Thu, 09 Dec 2021 03:57:47: end of X-cor INFO @ Thu, 09 Dec 2021 03:57:47: #2 finished! INFO @ Thu, 09 Dec 2021 03:57:47: #2 predicted fragment length is 188 bps INFO @ Thu, 09 Dec 2021 03:57:47: #2 alternative fragment length(s) may be 188 bps INFO @ Thu, 09 Dec 2021 03:57:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.20_model.r INFO @ Thu, 09 Dec 2021 03:57:47: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:57:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:58:08: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:58:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:58:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:58:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399027/SRX10399027.20_summits.bed INFO @ Thu, 09 Dec 2021 03:58:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (691 records, 4 fields): 23 millis CompletedMACS2peakCalling