Job ID = 14159143 SRX = SRX8976702 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: 00:13:41 16433460 reads; of these: 16433460 (100.00%) were paired; of these: 1439728 (8.76%) aligned concordantly 0 times 12986133 (79.02%) aligned concordantly exactly 1 time 2007599 (12.22%) aligned concordantly >1 times ---- 1439728 pairs aligned concordantly 0 times; of these: 972349 (67.54%) aligned discordantly 1 time ---- 467379 pairs aligned 0 times concordantly or discordantly; of these: 934758 mates make up the pairs; of these: 371970 (39.79%) aligned 0 times 297461 (31.82%) aligned exactly 1 time 265327 (28.38%) aligned >1 times 98.87% overall alignment rate Time searching: 00:13:41 Overall time: 00:13:41 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 16 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] 278441 / 15944266 = 0.0175 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 20:15:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.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 20:15:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:15:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:15:14: 1000000 INFO @ Wed, 08 Dec 2021 20:15:19: 2000000 INFO @ Wed, 08 Dec 2021 20:15:24: 3000000 INFO @ Wed, 08 Dec 2021 20:15:28: 4000000 INFO @ Wed, 08 Dec 2021 20:15:33: 5000000 INFO @ Wed, 08 Dec 2021 20:15:37: 6000000 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 20:15:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.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 20:15:39: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:15:39: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:15:42: 7000000 INFO @ Wed, 08 Dec 2021 20:15:44: 1000000 INFO @ Wed, 08 Dec 2021 20:15:47: 8000000 INFO @ Wed, 08 Dec 2021 20:15:49: 2000000 INFO @ Wed, 08 Dec 2021 20:15:52: 9000000 INFO @ Wed, 08 Dec 2021 20:15:54: 3000000 INFO @ Wed, 08 Dec 2021 20:15:57: 10000000 INFO @ Wed, 08 Dec 2021 20:15:59: 4000000 INFO @ Wed, 08 Dec 2021 20:16:02: 11000000 INFO @ Wed, 08 Dec 2021 20:16:04: 5000000 INFO @ Wed, 08 Dec 2021 20:16:06: 12000000 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 20:16:09: 6000000 INFO @ Wed, 08 Dec 2021 20:16:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.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 20:16:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:16:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:16:11: 13000000 INFO @ Wed, 08 Dec 2021 20:16:14: 7000000 INFO @ Wed, 08 Dec 2021 20:16:15: 1000000 INFO @ Wed, 08 Dec 2021 20:16:17: 14000000 INFO @ Wed, 08 Dec 2021 20:16:19: 8000000 INFO @ Wed, 08 Dec 2021 20:16:21: 2000000 INFO @ Wed, 08 Dec 2021 20:16:22: 15000000 INFO @ Wed, 08 Dec 2021 20:16:24: 9000000 INFO @ Wed, 08 Dec 2021 20:16:26: 3000000 INFO @ Wed, 08 Dec 2021 20:16:27: 16000000 INFO @ Wed, 08 Dec 2021 20:16:29: 10000000 INFO @ Wed, 08 Dec 2021 20:16:32: 4000000 INFO @ Wed, 08 Dec 2021 20:16:32: 17000000 INFO @ Wed, 08 Dec 2021 20:16:34: 11000000 INFO @ Wed, 08 Dec 2021 20:16:37: 18000000 INFO @ Wed, 08 Dec 2021 20:16:38: 5000000 INFO @ Wed, 08 Dec 2021 20:16:40: 12000000 INFO @ Wed, 08 Dec 2021 20:16:43: 19000000 INFO @ Wed, 08 Dec 2021 20:16:43: 6000000 INFO @ Wed, 08 Dec 2021 20:16:45: 13000000 INFO @ Wed, 08 Dec 2021 20:16:48: 20000000 INFO @ Wed, 08 Dec 2021 20:16:49: 7000000 INFO @ Wed, 08 Dec 2021 20:16:50: 14000000 INFO @ Wed, 08 Dec 2021 20:16:53: 21000000 INFO @ Wed, 08 Dec 2021 20:16:55: 15000000 INFO @ Wed, 08 Dec 2021 20:16:55: 8000000 INFO @ Wed, 08 Dec 2021 20:16:58: 22000000 INFO @ Wed, 08 Dec 2021 20:17:00: 16000000 INFO @ Wed, 08 Dec 2021 20:17:01: 9000000 INFO @ Wed, 08 Dec 2021 20:17:03: 23000000 INFO @ Wed, 08 Dec 2021 20:17:05: 17000000 INFO @ Wed, 08 Dec 2021 20:17:07: 10000000 INFO @ Wed, 08 Dec 2021 20:17:08: 24000000 INFO @ Wed, 08 Dec 2021 20:17:10: 18000000 INFO @ Wed, 08 Dec 2021 20:17:13: 11000000 INFO @ Wed, 08 Dec 2021 20:17:13: 25000000 INFO @ Wed, 08 Dec 2021 20:17:16: 19000000 INFO @ Wed, 08 Dec 2021 20:17:19: 26000000 INFO @ Wed, 08 Dec 2021 20:17:19: 12000000 INFO @ Wed, 08 Dec 2021 20:17:21: 20000000 INFO @ Wed, 08 Dec 2021 20:17:24: 27000000 INFO @ Wed, 08 Dec 2021 20:17:24: 13000000 INFO @ Wed, 08 Dec 2021 20:17:26: 21000000 INFO @ Wed, 08 Dec 2021 20:17:29: 28000000 INFO @ Wed, 08 Dec 2021 20:17:30: 14000000 INFO @ Wed, 08 Dec 2021 20:17:31: 22000000 INFO @ Wed, 08 Dec 2021 20:17:34: 29000000 INFO @ Wed, 08 Dec 2021 20:17:36: 15000000 INFO @ Wed, 08 Dec 2021 20:17:36: 23000000 INFO @ Wed, 08 Dec 2021 20:17:39: 30000000 INFO @ Wed, 08 Dec 2021 20:17:41: 24000000 INFO @ Wed, 08 Dec 2021 20:17:42: 16000000 INFO @ Wed, 08 Dec 2021 20:17:44: 31000000 INFO @ Wed, 08 Dec 2021 20:17:47: 25000000 INFO @ Wed, 08 Dec 2021 20:17:48: 17000000 INFO @ Wed, 08 Dec 2021 20:17:49: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:17:49: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:17:49: #1 total tags in treatment: 14725972 INFO @ Wed, 08 Dec 2021 20:17:49: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:17:49: #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 20:17:49: #1 tags after filtering in treatment: 13626760 INFO @ Wed, 08 Dec 2021 20:17:49: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:17:49: #1 finished! INFO @ Wed, 08 Dec 2021 20:17:49: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:17:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:17:50: #2 number of paired peaks: 327 WARNING @ Wed, 08 Dec 2021 20:17:50: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Wed, 08 Dec 2021 20:17:50: start model_add_line... INFO @ Wed, 08 Dec 2021 20:17:50: start X-correlation... INFO @ Wed, 08 Dec 2021 20:17:50: end of X-cor INFO @ Wed, 08 Dec 2021 20:17:50: #2 finished! INFO @ Wed, 08 Dec 2021 20:17:50: #2 predicted fragment length is 148 bps INFO @ Wed, 08 Dec 2021 20:17:50: #2 alternative fragment length(s) may be 4,148 bps INFO @ Wed, 08 Dec 2021 20:17:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.05_model.r INFO @ Wed, 08 Dec 2021 20:17:50: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:17:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:17:52: 26000000 INFO @ Wed, 08 Dec 2021 20:17:54: 18000000 INFO @ Wed, 08 Dec 2021 20:17:57: 27000000 INFO @ Wed, 08 Dec 2021 20:17:59: 19000000 INFO @ Wed, 08 Dec 2021 20:18:02: 28000000 INFO @ Wed, 08 Dec 2021 20:18:05: 20000000 INFO @ Wed, 08 Dec 2021 20:18:07: 29000000 INFO @ Wed, 08 Dec 2021 20:18:11: 21000000 INFO @ Wed, 08 Dec 2021 20:18:12: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:18:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:18:17: 22000000 INFO @ Wed, 08 Dec 2021 20:18:17: 31000000 INFO @ Wed, 08 Dec 2021 20:18:22: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:18:22: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:18:22: #1 total tags in treatment: 14725972 INFO @ Wed, 08 Dec 2021 20:18:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:18:22: #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 20:18:22: #1 tags after filtering in treatment: 13626760 INFO @ Wed, 08 Dec 2021 20:18:22: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:18:22: #1 finished! INFO @ Wed, 08 Dec 2021 20:18:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:18:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:18:23: 23000000 INFO @ Wed, 08 Dec 2021 20:18:23: #2 number of paired peaks: 327 WARNING @ Wed, 08 Dec 2021 20:18:23: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Wed, 08 Dec 2021 20:18:23: start model_add_line... INFO @ Wed, 08 Dec 2021 20:18:23: start X-correlation... INFO @ Wed, 08 Dec 2021 20:18:23: end of X-cor INFO @ Wed, 08 Dec 2021 20:18:23: #2 finished! INFO @ Wed, 08 Dec 2021 20:18:23: #2 predicted fragment length is 148 bps INFO @ Wed, 08 Dec 2021 20:18:23: #2 alternative fragment length(s) may be 4,148 bps INFO @ Wed, 08 Dec 2021 20:18:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.10_model.r INFO @ Wed, 08 Dec 2021 20:18:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:18:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:18:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:18:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:18:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.05_summits.bed INFO @ Wed, 08 Dec 2021 20:18:27: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (386 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:18:28: 24000000 INFO @ Wed, 08 Dec 2021 20:18:34: 25000000 INFO @ Wed, 08 Dec 2021 20:18:39: 26000000 INFO @ Wed, 08 Dec 2021 20:18:45: 27000000 INFO @ Wed, 08 Dec 2021 20:18:49: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:18:50: 28000000 INFO @ Wed, 08 Dec 2021 20:18:56: 29000000 INFO @ Wed, 08 Dec 2021 20:19:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:19:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:19:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.10_summits.bed INFO @ Wed, 08 Dec 2021 20:19:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:19:01: 30000000 INFO @ Wed, 08 Dec 2021 20:19:07: 31000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:19:12: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:19:12: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:19:12: #1 total tags in treatment: 14725972 INFO @ Wed, 08 Dec 2021 20:19:12: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:19:12: #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 20:19:12: #1 tags after filtering in treatment: 13626760 INFO @ Wed, 08 Dec 2021 20:19:12: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:19:12: #1 finished! INFO @ Wed, 08 Dec 2021 20:19:12: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:19:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:19:13: #2 number of paired peaks: 327 WARNING @ Wed, 08 Dec 2021 20:19:13: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Wed, 08 Dec 2021 20:19:13: start model_add_line... INFO @ Wed, 08 Dec 2021 20:19:13: start X-correlation... INFO @ Wed, 08 Dec 2021 20:19:13: end of X-cor INFO @ Wed, 08 Dec 2021 20:19:13: #2 finished! INFO @ Wed, 08 Dec 2021 20:19:13: #2 predicted fragment length is 148 bps INFO @ Wed, 08 Dec 2021 20:19:13: #2 alternative fragment length(s) may be 4,148 bps INFO @ Wed, 08 Dec 2021 20:19:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.20_model.r INFO @ Wed, 08 Dec 2021 20:19:13: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:19:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:19:39: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:19:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:19:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:19:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976702/SRX8976702.20_summits.bed INFO @ Wed, 08 Dec 2021 20:19:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (202 records, 4 fields): 1 millis CompletedMACS2peakCalling