Job ID = 14159426 SRX = SRX8976746 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:27:27 19954377 reads; of these: 19954377 (100.00%) were paired; of these: 2588946 (12.97%) aligned concordantly 0 times 12115555 (60.72%) aligned concordantly exactly 1 time 5249876 (26.31%) aligned concordantly >1 times ---- 2588946 pairs aligned concordantly 0 times; of these: 1478632 (57.11%) aligned discordantly 1 time ---- 1110314 pairs aligned 0 times concordantly or discordantly; of these: 2220628 mates make up the pairs; of these: 402916 (18.14%) aligned 0 times 582283 (26.22%) aligned exactly 1 time 1235429 (55.63%) aligned >1 times 98.99% overall alignment rate Time searching: 00:27:28 Overall time: 00:27:28 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] 1363406 / 18827027 = 0.0724 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 22:18:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.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 22:18:57: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:18:57: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:19:05: 1000000 INFO @ Wed, 08 Dec 2021 22:19:13: 2000000 INFO @ Wed, 08 Dec 2021 22:19:22: 3000000 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 22:19:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.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 22:19:27: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:19:27: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:19:30: 4000000 INFO @ Wed, 08 Dec 2021 22:19:37: 1000000 INFO @ Wed, 08 Dec 2021 22:19:38: 5000000 INFO @ Wed, 08 Dec 2021 22:19:46: 2000000 INFO @ Wed, 08 Dec 2021 22:19:47: 6000000 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 22:19:55: 7000000 INFO @ Wed, 08 Dec 2021 22:19:56: 3000000 INFO @ Wed, 08 Dec 2021 22:19:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.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 22:19:57: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:19:57: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:20:03: 8000000 INFO @ Wed, 08 Dec 2021 22:20:06: 1000000 INFO @ Wed, 08 Dec 2021 22:20:06: 4000000 INFO @ Wed, 08 Dec 2021 22:20:12: 9000000 INFO @ Wed, 08 Dec 2021 22:20:14: 2000000 INFO @ Wed, 08 Dec 2021 22:20:16: 5000000 INFO @ Wed, 08 Dec 2021 22:20:20: 10000000 INFO @ Wed, 08 Dec 2021 22:20:23: 3000000 INFO @ Wed, 08 Dec 2021 22:20:25: 6000000 INFO @ Wed, 08 Dec 2021 22:20:28: 11000000 INFO @ Wed, 08 Dec 2021 22:20:31: 4000000 INFO @ Wed, 08 Dec 2021 22:20:35: 7000000 INFO @ Wed, 08 Dec 2021 22:20:37: 12000000 INFO @ Wed, 08 Dec 2021 22:20:39: 5000000 INFO @ Wed, 08 Dec 2021 22:20:45: 8000000 INFO @ Wed, 08 Dec 2021 22:20:45: 13000000 INFO @ Wed, 08 Dec 2021 22:20:48: 6000000 INFO @ Wed, 08 Dec 2021 22:20:54: 14000000 INFO @ Wed, 08 Dec 2021 22:20:54: 9000000 INFO @ Wed, 08 Dec 2021 22:20:56: 7000000 INFO @ Wed, 08 Dec 2021 22:21:02: 15000000 INFO @ Wed, 08 Dec 2021 22:21:05: 10000000 INFO @ Wed, 08 Dec 2021 22:21:05: 8000000 INFO @ Wed, 08 Dec 2021 22:21:11: 16000000 INFO @ Wed, 08 Dec 2021 22:21:14: 9000000 INFO @ Wed, 08 Dec 2021 22:21:15: 11000000 INFO @ Wed, 08 Dec 2021 22:21:19: 17000000 INFO @ Wed, 08 Dec 2021 22:21:22: 10000000 INFO @ Wed, 08 Dec 2021 22:21:25: 12000000 INFO @ Wed, 08 Dec 2021 22:21:28: 18000000 INFO @ Wed, 08 Dec 2021 22:21:31: 11000000 INFO @ Wed, 08 Dec 2021 22:21:35: 13000000 INFO @ Wed, 08 Dec 2021 22:21:37: 19000000 INFO @ Wed, 08 Dec 2021 22:21:40: 12000000 INFO @ Wed, 08 Dec 2021 22:21:45: 14000000 INFO @ Wed, 08 Dec 2021 22:21:45: 20000000 INFO @ Wed, 08 Dec 2021 22:21:48: 13000000 INFO @ Wed, 08 Dec 2021 22:21:54: 21000000 INFO @ Wed, 08 Dec 2021 22:21:55: 15000000 INFO @ Wed, 08 Dec 2021 22:21:57: 14000000 INFO @ Wed, 08 Dec 2021 22:22:03: 22000000 INFO @ Wed, 08 Dec 2021 22:22:05: 15000000 INFO @ Wed, 08 Dec 2021 22:22:06: 16000000 INFO @ Wed, 08 Dec 2021 22:22:12: 23000000 INFO @ Wed, 08 Dec 2021 22:22:14: 16000000 INFO @ Wed, 08 Dec 2021 22:22:16: 17000000 INFO @ Wed, 08 Dec 2021 22:22:21: 24000000 INFO @ Wed, 08 Dec 2021 22:22:22: 17000000 INFO @ Wed, 08 Dec 2021 22:22:26: 18000000 INFO @ Wed, 08 Dec 2021 22:22:29: 25000000 INFO @ Wed, 08 Dec 2021 22:22:31: 18000000 INFO @ Wed, 08 Dec 2021 22:22:36: 19000000 INFO @ Wed, 08 Dec 2021 22:22:38: 26000000 INFO @ Wed, 08 Dec 2021 22:22:39: 19000000 INFO @ Wed, 08 Dec 2021 22:22:46: 27000000 INFO @ Wed, 08 Dec 2021 22:22:46: 20000000 INFO @ Wed, 08 Dec 2021 22:22:48: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:22:54: 28000000 INFO @ Wed, 08 Dec 2021 22:22:57: 21000000 INFO @ Wed, 08 Dec 2021 22:22:57: 21000000 INFO @ Wed, 08 Dec 2021 22:23:02: 29000000 INFO @ Wed, 08 Dec 2021 22:23:06: 22000000 INFO @ Wed, 08 Dec 2021 22:23:07: 22000000 INFO @ Wed, 08 Dec 2021 22:23:11: 30000000 INFO @ Wed, 08 Dec 2021 22:23:15: 23000000 INFO @ Wed, 08 Dec 2021 22:23:17: 23000000 INFO @ Wed, 08 Dec 2021 22:23:19: 31000000 INFO @ Wed, 08 Dec 2021 22:23:23: 24000000 INFO @ Wed, 08 Dec 2021 22:23:28: 24000000 INFO @ Wed, 08 Dec 2021 22:23:28: 32000000 INFO @ Wed, 08 Dec 2021 22:23:31: 25000000 INFO @ Wed, 08 Dec 2021 22:23:36: 33000000 INFO @ Wed, 08 Dec 2021 22:23:38: 25000000 INFO @ Wed, 08 Dec 2021 22:23:40: 26000000 INFO @ Wed, 08 Dec 2021 22:23:45: 34000000 INFO @ Wed, 08 Dec 2021 22:23:47: 26000000 INFO @ Wed, 08 Dec 2021 22:23:48: 27000000 INFO @ Wed, 08 Dec 2021 22:23:53: 35000000 INFO @ Wed, 08 Dec 2021 22:23:56: 28000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:23:57: 27000000 INFO @ Wed, 08 Dec 2021 22:24:02: 36000000 INFO @ Wed, 08 Dec 2021 22:24:03: 29000000 INFO @ Wed, 08 Dec 2021 22:24:06: 28000000 INFO @ Wed, 08 Dec 2021 22:24:08: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:24:08: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:24:08: #1 total tags in treatment: 16062735 INFO @ Wed, 08 Dec 2021 22:24:08: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:24:08: #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 22:24:08: #1 tags after filtering in treatment: 12106972 INFO @ Wed, 08 Dec 2021 22:24:08: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 08 Dec 2021 22:24:08: #1 finished! INFO @ Wed, 08 Dec 2021 22:24:08: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:24:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:24:10: #2 number of paired peaks: 4462 INFO @ Wed, 08 Dec 2021 22:24:10: start model_add_line... INFO @ Wed, 08 Dec 2021 22:24:10: start X-correlation... INFO @ Wed, 08 Dec 2021 22:24:10: end of X-cor INFO @ Wed, 08 Dec 2021 22:24:10: #2 finished! INFO @ Wed, 08 Dec 2021 22:24:10: #2 predicted fragment length is 245 bps INFO @ Wed, 08 Dec 2021 22:24:10: #2 alternative fragment length(s) may be 1,225,229,245,261 bps INFO @ Wed, 08 Dec 2021 22:24:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.05_model.r INFO @ Wed, 08 Dec 2021 22:24:10: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:24:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:24:11: 30000000 INFO @ Wed, 08 Dec 2021 22:24:16: 29000000 INFO @ Wed, 08 Dec 2021 22:24:19: 31000000 INFO @ Wed, 08 Dec 2021 22:24:26: 30000000 INFO @ Wed, 08 Dec 2021 22:24:27: 32000000 INFO @ Wed, 08 Dec 2021 22:24:35: 33000000 INFO @ Wed, 08 Dec 2021 22:24:35: 31000000 INFO @ Wed, 08 Dec 2021 22:24:44: 34000000 INFO @ Wed, 08 Dec 2021 22:24:45: 32000000 INFO @ Wed, 08 Dec 2021 22:24:52: 35000000 INFO @ Wed, 08 Dec 2021 22:24:55: 33000000 INFO @ Wed, 08 Dec 2021 22:24:59: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:25:00: 36000000 INFO @ Wed, 08 Dec 2021 22:25:05: 34000000 INFO @ Wed, 08 Dec 2021 22:25:07: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:25:07: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:25:07: #1 total tags in treatment: 16062735 INFO @ Wed, 08 Dec 2021 22:25:07: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:25:07: #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 22:25:07: #1 tags after filtering in treatment: 12106972 INFO @ Wed, 08 Dec 2021 22:25:07: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 08 Dec 2021 22:25:07: #1 finished! INFO @ Wed, 08 Dec 2021 22:25:07: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:25:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:25:09: #2 number of paired peaks: 4462 INFO @ Wed, 08 Dec 2021 22:25:09: start model_add_line... INFO @ Wed, 08 Dec 2021 22:25:09: start X-correlation... INFO @ Wed, 08 Dec 2021 22:25:09: end of X-cor INFO @ Wed, 08 Dec 2021 22:25:09: #2 finished! INFO @ Wed, 08 Dec 2021 22:25:09: #2 predicted fragment length is 245 bps INFO @ Wed, 08 Dec 2021 22:25:09: #2 alternative fragment length(s) may be 1,225,229,245,261 bps INFO @ Wed, 08 Dec 2021 22:25:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.20_model.r INFO @ Wed, 08 Dec 2021 22:25:09: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:25:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:25:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:25:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:25:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.05_summits.bed INFO @ Wed, 08 Dec 2021 22:25:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2455 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:25:15: 35000000 INFO @ Wed, 08 Dec 2021 22:25:25: 36000000 INFO @ Wed, 08 Dec 2021 22:25:32: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:25:32: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:25:32: #1 total tags in treatment: 16062735 INFO @ Wed, 08 Dec 2021 22:25:32: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:25:32: #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 22:25:33: #1 tags after filtering in treatment: 12106972 INFO @ Wed, 08 Dec 2021 22:25:33: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 08 Dec 2021 22:25:33: #1 finished! INFO @ Wed, 08 Dec 2021 22:25:33: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:25:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:25:34: #2 number of paired peaks: 4462 INFO @ Wed, 08 Dec 2021 22:25:34: start model_add_line... INFO @ Wed, 08 Dec 2021 22:25:34: start X-correlation... INFO @ Wed, 08 Dec 2021 22:25:34: end of X-cor INFO @ Wed, 08 Dec 2021 22:25:34: #2 finished! INFO @ Wed, 08 Dec 2021 22:25:34: #2 predicted fragment length is 245 bps INFO @ Wed, 08 Dec 2021 22:25:34: #2 alternative fragment length(s) may be 1,225,229,245,261 bps INFO @ Wed, 08 Dec 2021 22:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.10_model.r INFO @ Wed, 08 Dec 2021 22:25:34: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:25:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:26:00: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:26:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:26:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:26:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.20_summits.bed INFO @ Wed, 08 Dec 2021 22:26:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:26:23: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:26:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:26:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:26:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976746/SRX8976746.10_summits.bed INFO @ Wed, 08 Dec 2021 22:26:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1105 records, 4 fields): 5 millis CompletedMACS2peakCalling