Job ID = 14158808 SRX = SRX10342586 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED 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: 00:12:36 16807290 reads; of these: 16807290 (100.00%) were paired; of these: 4478506 (26.65%) aligned concordantly 0 times 10433873 (62.08%) aligned concordantly exactly 1 time 1894911 (11.27%) aligned concordantly >1 times ---- 4478506 pairs aligned concordantly 0 times; of these: 3511574 (78.41%) aligned discordantly 1 time ---- 966932 pairs aligned 0 times concordantly or discordantly; of these: 1933864 mates make up the pairs; of these: 510827 (26.41%) aligned 0 times 564983 (29.22%) aligned exactly 1 time 858054 (44.37%) aligned >1 times 98.48% overall alignment rate Time searching: 00:12:36 Overall time: 00:12:36 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 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1195459 / 15827230 = 0.0755 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 @ Wed, 08 Dec 2021 18:21:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.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 @ Wed, 08 Dec 2021 18:21:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:21:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:21:35: 1000000 INFO @ Wed, 08 Dec 2021 18:21:42: 2000000 INFO @ Wed, 08 Dec 2021 18:21:48: 3000000 INFO @ Wed, 08 Dec 2021 18:21:55: 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 @ Wed, 08 Dec 2021 18:21:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.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 @ Wed, 08 Dec 2021 18:21:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:21:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:22:01: 5000000 INFO @ Wed, 08 Dec 2021 18:22:06: 1000000 INFO @ Wed, 08 Dec 2021 18:22:09: 6000000 INFO @ Wed, 08 Dec 2021 18:22:12: 2000000 INFO @ Wed, 08 Dec 2021 18:22:16: 7000000 INFO @ Wed, 08 Dec 2021 18:22:18: 3000000 INFO @ Wed, 08 Dec 2021 18:22:23: 8000000 INFO @ Wed, 08 Dec 2021 18:22:25: 4000000 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 @ Wed, 08 Dec 2021 18:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.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 @ Wed, 08 Dec 2021 18:22:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:22:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:22:30: 9000000 INFO @ Wed, 08 Dec 2021 18:22:31: 5000000 INFO @ Wed, 08 Dec 2021 18:22:35: 1000000 INFO @ Wed, 08 Dec 2021 18:22:37: 10000000 INFO @ Wed, 08 Dec 2021 18:22:37: 6000000 INFO @ Wed, 08 Dec 2021 18:22:42: 2000000 INFO @ Wed, 08 Dec 2021 18:22:44: 7000000 INFO @ Wed, 08 Dec 2021 18:22:45: 11000000 INFO @ Wed, 08 Dec 2021 18:22:48: 3000000 INFO @ Wed, 08 Dec 2021 18:22:50: 8000000 INFO @ Wed, 08 Dec 2021 18:22:52: 12000000 INFO @ Wed, 08 Dec 2021 18:22:54: 4000000 INFO @ Wed, 08 Dec 2021 18:22:57: 9000000 INFO @ Wed, 08 Dec 2021 18:22:59: 13000000 INFO @ Wed, 08 Dec 2021 18:23:01: 5000000 INFO @ Wed, 08 Dec 2021 18:23:03: 10000000 INFO @ Wed, 08 Dec 2021 18:23:06: 14000000 INFO @ Wed, 08 Dec 2021 18:23:07: 6000000 INFO @ Wed, 08 Dec 2021 18:23:09: 11000000 INFO @ Wed, 08 Dec 2021 18:23:13: 15000000 INFO @ Wed, 08 Dec 2021 18:23:13: 7000000 INFO @ Wed, 08 Dec 2021 18:23:16: 12000000 INFO @ Wed, 08 Dec 2021 18:23:20: 8000000 INFO @ Wed, 08 Dec 2021 18:23:20: 16000000 INFO @ Wed, 08 Dec 2021 18:23:22: 13000000 INFO @ Wed, 08 Dec 2021 18:23:26: 9000000 INFO @ Wed, 08 Dec 2021 18:23:28: 17000000 INFO @ Wed, 08 Dec 2021 18:23:28: 14000000 INFO @ Wed, 08 Dec 2021 18:23:32: 10000000 INFO @ Wed, 08 Dec 2021 18:23:35: 15000000 INFO @ Wed, 08 Dec 2021 18:23:35: 18000000 INFO @ Wed, 08 Dec 2021 18:23:39: 11000000 INFO @ Wed, 08 Dec 2021 18:23:41: 16000000 INFO @ Wed, 08 Dec 2021 18:23:42: 19000000 INFO @ Wed, 08 Dec 2021 18:23:45: 12000000 INFO @ Wed, 08 Dec 2021 18:23:47: 17000000 INFO @ Wed, 08 Dec 2021 18:23:49: 20000000 INFO @ Wed, 08 Dec 2021 18:23:51: 13000000 INFO @ Wed, 08 Dec 2021 18:23:54: 18000000 INFO @ Wed, 08 Dec 2021 18:23:56: 21000000 INFO @ Wed, 08 Dec 2021 18:23:57: 14000000 INFO @ Wed, 08 Dec 2021 18:24:00: 19000000 INFO @ Wed, 08 Dec 2021 18:24:04: 22000000 INFO @ Wed, 08 Dec 2021 18:24:04: 15000000 INFO @ Wed, 08 Dec 2021 18:24:06: 20000000 INFO @ Wed, 08 Dec 2021 18:24:10: 16000000 INFO @ Wed, 08 Dec 2021 18:24:11: 23000000 INFO @ Wed, 08 Dec 2021 18:24:12: 21000000 INFO @ Wed, 08 Dec 2021 18:24:16: 17000000 INFO @ Wed, 08 Dec 2021 18:24:18: 24000000 INFO @ Wed, 08 Dec 2021 18:24:19: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:24:23: 18000000 INFO @ Wed, 08 Dec 2021 18:24:25: 23000000 INFO @ Wed, 08 Dec 2021 18:24:25: 25000000 INFO @ Wed, 08 Dec 2021 18:24:29: 19000000 INFO @ Wed, 08 Dec 2021 18:24:31: 24000000 INFO @ Wed, 08 Dec 2021 18:24:32: 26000000 INFO @ Wed, 08 Dec 2021 18:24:35: 20000000 INFO @ Wed, 08 Dec 2021 18:24:38: 25000000 INFO @ Wed, 08 Dec 2021 18:24:39: 27000000 INFO @ Wed, 08 Dec 2021 18:24:42: 21000000 INFO @ Wed, 08 Dec 2021 18:24:44: 26000000 INFO @ Wed, 08 Dec 2021 18:24:46: 28000000 INFO @ Wed, 08 Dec 2021 18:24:48: 22000000 INFO @ Wed, 08 Dec 2021 18:24:50: 27000000 INFO @ Wed, 08 Dec 2021 18:24:54: 29000000 INFO @ Wed, 08 Dec 2021 18:24:54: 23000000 INFO @ Wed, 08 Dec 2021 18:24:56: 28000000 INFO @ Wed, 08 Dec 2021 18:25:00: 24000000 INFO @ Wed, 08 Dec 2021 18:25:01: 30000000 INFO @ Wed, 08 Dec 2021 18:25:03: 29000000 INFO @ Wed, 08 Dec 2021 18:25:05: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:25:05: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:25:05: #1 total tags in treatment: 11340652 INFO @ Wed, 08 Dec 2021 18:25:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:25:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 18:25:06: #1 tags after filtering in treatment: 10341861 INFO @ Wed, 08 Dec 2021 18:25:06: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 18:25:06: #1 finished! INFO @ Wed, 08 Dec 2021 18:25:06: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:25:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:25:06: #2 number of paired peaks: 492 WARNING @ Wed, 08 Dec 2021 18:25:06: Fewer paired peaks (492) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 492 pairs to build model! INFO @ Wed, 08 Dec 2021 18:25:06: start model_add_line... INFO @ Wed, 08 Dec 2021 18:25:06: start X-correlation... INFO @ Wed, 08 Dec 2021 18:25:06: end of X-cor INFO @ Wed, 08 Dec 2021 18:25:06: #2 finished! INFO @ Wed, 08 Dec 2021 18:25:06: #2 predicted fragment length is 114 bps INFO @ Wed, 08 Dec 2021 18:25:06: #2 alternative fragment length(s) may be 4,114,123,128 bps INFO @ Wed, 08 Dec 2021 18:25:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.05_model.r INFO @ Wed, 08 Dec 2021 18:25:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:25:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:25:07: 25000000 INFO @ Wed, 08 Dec 2021 18:25:09: 30000000 INFO @ Wed, 08 Dec 2021 18:25:13: 26000000 INFO @ Wed, 08 Dec 2021 18:25:13: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:25:13: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:25:13: #1 total tags in treatment: 11340652 INFO @ Wed, 08 Dec 2021 18:25:13: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:25:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 18:25:13: #1 tags after filtering in treatment: 10341861 INFO @ Wed, 08 Dec 2021 18:25:13: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 18:25:13: #1 finished! INFO @ Wed, 08 Dec 2021 18:25:13: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:25:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:25:14: #2 number of paired peaks: 492 WARNING @ Wed, 08 Dec 2021 18:25:14: Fewer paired peaks (492) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 492 pairs to build model! INFO @ Wed, 08 Dec 2021 18:25:14: start model_add_line... INFO @ Wed, 08 Dec 2021 18:25:14: start X-correlation... INFO @ Wed, 08 Dec 2021 18:25:14: end of X-cor INFO @ Wed, 08 Dec 2021 18:25:14: #2 finished! INFO @ Wed, 08 Dec 2021 18:25:14: #2 predicted fragment length is 114 bps INFO @ Wed, 08 Dec 2021 18:25:14: #2 alternative fragment length(s) may be 4,114,123,128 bps INFO @ Wed, 08 Dec 2021 18:25:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.10_model.r INFO @ Wed, 08 Dec 2021 18:25:14: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:25:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:25:19: 27000000 INFO @ Wed, 08 Dec 2021 18:25:24: 28000000 INFO @ Wed, 08 Dec 2021 18:25:26: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:25:30: 29000000 INFO @ Wed, 08 Dec 2021 18:25:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:25:35: 30000000 INFO @ Wed, 08 Dec 2021 18:25:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:25:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:25:39: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:25:39: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:25:39: #1 total tags in treatment: 11340652 INFO @ Wed, 08 Dec 2021 18:25:39: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:25:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 18:25:39: #1 tags after filtering in treatment: 10341861 INFO @ Wed, 08 Dec 2021 18:25:39: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 18:25:39: #1 finished! INFO @ Wed, 08 Dec 2021 18:25:39: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:25:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:25:40: #2 number of paired peaks: 492 WARNING @ Wed, 08 Dec 2021 18:25:40: Fewer paired peaks (492) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 492 pairs to build model! INFO @ Wed, 08 Dec 2021 18:25:40: start model_add_line... INFO @ Wed, 08 Dec 2021 18:25:40: start X-correlation... INFO @ Wed, 08 Dec 2021 18:25:40: end of X-cor INFO @ Wed, 08 Dec 2021 18:25:40: #2 finished! INFO @ Wed, 08 Dec 2021 18:25:40: #2 predicted fragment length is 114 bps INFO @ Wed, 08 Dec 2021 18:25:40: #2 alternative fragment length(s) may be 4,114,123,128 bps INFO @ Wed, 08 Dec 2021 18:25:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.20_model.r INFO @ Wed, 08 Dec 2021 18:25:40: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:25:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:25:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:25:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:25:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.10_summits.bed INFO @ Wed, 08 Dec 2021 18:25:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (332 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:25:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.05_summits.bed INFO @ Wed, 08 Dec 2021 18:25:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (436 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:26:00: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:26:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:26:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:26:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342586/SRX10342586.20_summits.bed INFO @ Wed, 08 Dec 2021 18:26:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (218 records, 4 fields): 2 millis CompletedMACS2peakCalling