Job ID = 14160453 SRX = SRX10398999 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: 00:03:25 17744254 reads; of these: 17744254 (100.00%) were unpaired; of these: 5947108 (33.52%) aligned 0 times 9850277 (55.51%) aligned exactly 1 time 1946869 (10.97%) aligned >1 times 66.48% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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] 1667995 / 11797146 = 0.1414 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 02:42:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.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 02:42:20: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:42:20: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:42:26: 1000000 INFO @ Thu, 09 Dec 2021 02:42:31: 2000000 INFO @ Thu, 09 Dec 2021 02:42:36: 3000000 INFO @ Thu, 09 Dec 2021 02:42:41: 4000000 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 02:42:47: 5000000 INFO @ Thu, 09 Dec 2021 02:42:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.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 02:42:48: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:42:48: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:42:52: 6000000 INFO @ Thu, 09 Dec 2021 02:42:54: 1000000 INFO @ Thu, 09 Dec 2021 02:42:57: 7000000 INFO @ Thu, 09 Dec 2021 02:43:01: 2000000 INFO @ Thu, 09 Dec 2021 02:43:03: 8000000 INFO @ Thu, 09 Dec 2021 02:43:07: 3000000 INFO @ Thu, 09 Dec 2021 02:43:08: 9000000 INFO @ Thu, 09 Dec 2021 02:43:13: 4000000 INFO @ Thu, 09 Dec 2021 02:43:14: 10000000 INFO @ Thu, 09 Dec 2021 02:43:14: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:43:14: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:43:14: #1 total tags in treatment: 10129151 INFO @ Thu, 09 Dec 2021 02:43:14: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:43:14: #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 02:43:15: #1 tags after filtering in treatment: 10129151 INFO @ Thu, 09 Dec 2021 02:43:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:43:15: #1 finished! INFO @ Thu, 09 Dec 2021 02:43:15: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:43:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:43:15: #2 number of paired peaks: 670 WARNING @ Thu, 09 Dec 2021 02:43:15: Fewer paired peaks (670) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 670 pairs to build model! INFO @ Thu, 09 Dec 2021 02:43:15: start model_add_line... INFO @ Thu, 09 Dec 2021 02:43:15: start X-correlation... INFO @ Thu, 09 Dec 2021 02:43:15: end of X-cor INFO @ Thu, 09 Dec 2021 02:43:15: #2 finished! INFO @ Thu, 09 Dec 2021 02:43:15: #2 predicted fragment length is 140 bps INFO @ Thu, 09 Dec 2021 02:43:15: #2 alternative fragment length(s) may be 140 bps INFO @ Thu, 09 Dec 2021 02:43:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.05_model.r INFO @ Thu, 09 Dec 2021 02:43:15: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:43:15: #3 Pre-compute pvalue-qvalue table... 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 02:43:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.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 02:43:18: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:43:18: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:43:19: 5000000 INFO @ Thu, 09 Dec 2021 02:43:24: 1000000 INFO @ Thu, 09 Dec 2021 02:43:26: 6000000 INFO @ Thu, 09 Dec 2021 02:43:31: 2000000 INFO @ Thu, 09 Dec 2021 02:43:32: 7000000 INFO @ Thu, 09 Dec 2021 02:43:37: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:43:37: 3000000 INFO @ Thu, 09 Dec 2021 02:43:38: 8000000 INFO @ Thu, 09 Dec 2021 02:43:43: 4000000 INFO @ Thu, 09 Dec 2021 02:43:44: 9000000 INFO @ Thu, 09 Dec 2021 02:43:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:43:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:43:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.05_summits.bed INFO @ Thu, 09 Dec 2021 02:43:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2177 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:43:50: 5000000 INFO @ Thu, 09 Dec 2021 02:43:50: 10000000 INFO @ Thu, 09 Dec 2021 02:43:51: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:43:51: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:43:51: #1 total tags in treatment: 10129151 INFO @ Thu, 09 Dec 2021 02:43:51: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:43:51: #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 02:43:51: #1 tags after filtering in treatment: 10129151 INFO @ Thu, 09 Dec 2021 02:43:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:43:51: #1 finished! INFO @ Thu, 09 Dec 2021 02:43:51: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:43:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:43:51: #2 number of paired peaks: 670 WARNING @ Thu, 09 Dec 2021 02:43:51: Fewer paired peaks (670) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 670 pairs to build model! INFO @ Thu, 09 Dec 2021 02:43:51: start model_add_line... INFO @ Thu, 09 Dec 2021 02:43:52: start X-correlation... INFO @ Thu, 09 Dec 2021 02:43:52: end of X-cor INFO @ Thu, 09 Dec 2021 02:43:52: #2 finished! INFO @ Thu, 09 Dec 2021 02:43:52: #2 predicted fragment length is 140 bps INFO @ Thu, 09 Dec 2021 02:43:52: #2 alternative fragment length(s) may be 140 bps INFO @ Thu, 09 Dec 2021 02:43:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.10_model.r INFO @ Thu, 09 Dec 2021 02:43:52: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:43:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:43:56: 6000000 INFO @ Thu, 09 Dec 2021 02:44:02: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:44:08: 8000000 INFO @ Thu, 09 Dec 2021 02:44:13: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:44:14: 9000000 INFO @ Thu, 09 Dec 2021 02:44:20: 10000000 INFO @ Thu, 09 Dec 2021 02:44:20: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:44:20: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:44:20: #1 total tags in treatment: 10129151 INFO @ Thu, 09 Dec 2021 02:44:20: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:44:20: #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 02:44:21: #1 tags after filtering in treatment: 10129151 INFO @ Thu, 09 Dec 2021 02:44:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 02:44:21: #1 finished! INFO @ Thu, 09 Dec 2021 02:44:21: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:44:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:44:21: #2 number of paired peaks: 670 WARNING @ Thu, 09 Dec 2021 02:44:21: Fewer paired peaks (670) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 670 pairs to build model! INFO @ Thu, 09 Dec 2021 02:44:21: start model_add_line... INFO @ Thu, 09 Dec 2021 02:44:21: start X-correlation... INFO @ Thu, 09 Dec 2021 02:44:21: end of X-cor INFO @ Thu, 09 Dec 2021 02:44:21: #2 finished! INFO @ Thu, 09 Dec 2021 02:44:21: #2 predicted fragment length is 140 bps INFO @ Thu, 09 Dec 2021 02:44:21: #2 alternative fragment length(s) may be 140 bps INFO @ Thu, 09 Dec 2021 02:44:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.20_model.r INFO @ Thu, 09 Dec 2021 02:44:21: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:44:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:44:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:44:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:44:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.10_summits.bed INFO @ Thu, 09 Dec 2021 02:44:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1323 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:44:42: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:44:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:44:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:44:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10398999/SRX10398999.20_summits.bed INFO @ Thu, 09 Dec 2021 02:44:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (792 records, 4 fields): 2 millis CompletedMACS2peakCalling