Job ID = 14159607 SRX = SRX8976689 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: 00:18:40 14573006 reads; of these: 14573006 (100.00%) were paired; of these: 1808897 (12.41%) aligned concordantly 0 times 9339729 (64.09%) aligned concordantly exactly 1 time 3424380 (23.50%) aligned concordantly >1 times ---- 1808897 pairs aligned concordantly 0 times; of these: 1057737 (58.47%) aligned discordantly 1 time ---- 751160 pairs aligned 0 times concordantly or discordantly; of these: 1502320 mates make up the pairs; of these: 415948 (27.69%) aligned 0 times 349334 (23.25%) aligned exactly 1 time 737038 (49.06%) aligned >1 times 98.57% overall alignment rate Time searching: 00:18:40 Overall time: 00:18:40 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] 1074694 / 13811273 = 0.0778 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 23:45:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.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 23:45:58: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:45:58: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:46:04: 1000000 INFO @ Wed, 08 Dec 2021 23:46:11: 2000000 INFO @ Wed, 08 Dec 2021 23:46:18: 3000000 INFO @ Wed, 08 Dec 2021 23:46:24: 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 23:46:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.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 23:46:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:46:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:46:31: 5000000 INFO @ Wed, 08 Dec 2021 23:46:36: 1000000 INFO @ Wed, 08 Dec 2021 23:46:38: 6000000 INFO @ Wed, 08 Dec 2021 23:46:44: 2000000 INFO @ Wed, 08 Dec 2021 23:46:45: 7000000 INFO @ Wed, 08 Dec 2021 23:46:52: 8000000 INFO @ Wed, 08 Dec 2021 23:46:52: 3000000 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 23:46:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.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 23:46:58: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:46:58: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:46:58: 9000000 INFO @ Wed, 08 Dec 2021 23:47:01: 4000000 INFO @ Wed, 08 Dec 2021 23:47:05: 10000000 INFO @ Wed, 08 Dec 2021 23:47:06: 1000000 INFO @ Wed, 08 Dec 2021 23:47:09: 5000000 INFO @ Wed, 08 Dec 2021 23:47:13: 11000000 INFO @ Wed, 08 Dec 2021 23:47:15: 2000000 INFO @ Wed, 08 Dec 2021 23:47:17: 6000000 INFO @ Wed, 08 Dec 2021 23:47:20: 12000000 INFO @ Wed, 08 Dec 2021 23:47:23: 3000000 INFO @ Wed, 08 Dec 2021 23:47:26: 7000000 INFO @ Wed, 08 Dec 2021 23:47:27: 13000000 INFO @ Wed, 08 Dec 2021 23:47:32: 4000000 INFO @ Wed, 08 Dec 2021 23:47:34: 8000000 INFO @ Wed, 08 Dec 2021 23:47:34: 14000000 INFO @ Wed, 08 Dec 2021 23:47:40: 5000000 INFO @ Wed, 08 Dec 2021 23:47:41: 15000000 INFO @ Wed, 08 Dec 2021 23:47:43: 9000000 INFO @ Wed, 08 Dec 2021 23:47:48: 6000000 INFO @ Wed, 08 Dec 2021 23:47:48: 16000000 INFO @ Wed, 08 Dec 2021 23:47:51: 10000000 INFO @ Wed, 08 Dec 2021 23:47:55: 17000000 INFO @ Wed, 08 Dec 2021 23:47:57: 7000000 INFO @ Wed, 08 Dec 2021 23:48:00: 11000000 INFO @ Wed, 08 Dec 2021 23:48:02: 18000000 INFO @ Wed, 08 Dec 2021 23:48:05: 8000000 INFO @ Wed, 08 Dec 2021 23:48:08: 12000000 INFO @ Wed, 08 Dec 2021 23:48:09: 19000000 INFO @ Wed, 08 Dec 2021 23:48:14: 9000000 INFO @ Wed, 08 Dec 2021 23:48:16: 20000000 INFO @ Wed, 08 Dec 2021 23:48:17: 13000000 INFO @ Wed, 08 Dec 2021 23:48:23: 10000000 INFO @ Wed, 08 Dec 2021 23:48:23: 21000000 INFO @ Wed, 08 Dec 2021 23:48:26: 14000000 INFO @ Wed, 08 Dec 2021 23:48:30: 22000000 INFO @ Wed, 08 Dec 2021 23:48:31: 11000000 INFO @ Wed, 08 Dec 2021 23:48:34: 15000000 INFO @ Wed, 08 Dec 2021 23:48:37: 23000000 INFO @ Wed, 08 Dec 2021 23:48:40: 12000000 INFO @ Wed, 08 Dec 2021 23:48:43: 16000000 INFO @ Wed, 08 Dec 2021 23:48:44: 24000000 INFO @ Wed, 08 Dec 2021 23:48:48: 13000000 INFO @ Wed, 08 Dec 2021 23:48:51: 17000000 INFO @ Wed, 08 Dec 2021 23:48:51: 25000000 INFO @ Wed, 08 Dec 2021 23:48:56: 14000000 INFO @ Wed, 08 Dec 2021 23:48:58: 26000000 INFO @ Wed, 08 Dec 2021 23:49:00: 18000000 INFO @ Wed, 08 Dec 2021 23:49:02: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 23:49:02: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 23:49:02: #1 total tags in treatment: 11744783 INFO @ Wed, 08 Dec 2021 23:49:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:49:02: #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 23:49:03: #1 tags after filtering in treatment: 9539163 INFO @ Wed, 08 Dec 2021 23:49:03: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 23:49:03: #1 finished! INFO @ Wed, 08 Dec 2021 23:49:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:49:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:49:04: #2 number of paired peaks: 3899 INFO @ Wed, 08 Dec 2021 23:49:04: start model_add_line... INFO @ Wed, 08 Dec 2021 23:49:04: start X-correlation... INFO @ Wed, 08 Dec 2021 23:49:04: end of X-cor INFO @ Wed, 08 Dec 2021 23:49:04: #2 finished! INFO @ Wed, 08 Dec 2021 23:49:04: #2 predicted fragment length is 257 bps INFO @ Wed, 08 Dec 2021 23:49:04: #2 alternative fragment length(s) may be 2,257 bps INFO @ Wed, 08 Dec 2021 23:49:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.05_model.r INFO @ Wed, 08 Dec 2021 23:49:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:49:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:49:05: 15000000 INFO @ Wed, 08 Dec 2021 23:49:08: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:49:14: 16000000 INFO @ Wed, 08 Dec 2021 23:49:17: 20000000 INFO @ Wed, 08 Dec 2021 23:49:22: 17000000 INFO @ Wed, 08 Dec 2021 23:49:25: 21000000 INFO @ Wed, 08 Dec 2021 23:49:30: 18000000 INFO @ Wed, 08 Dec 2021 23:49:33: 22000000 INFO @ Wed, 08 Dec 2021 23:49:39: 19000000 INFO @ Wed, 08 Dec 2021 23:49:42: 23000000 INFO @ Wed, 08 Dec 2021 23:49:42: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:49:47: 20000000 INFO @ Wed, 08 Dec 2021 23:49:50: 24000000 INFO @ Wed, 08 Dec 2021 23:49:55: 21000000 INFO @ Wed, 08 Dec 2021 23:49:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:49:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:49:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.05_summits.bed INFO @ Wed, 08 Dec 2021 23:49:55: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1721 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:49:58: 25000000 INFO @ Wed, 08 Dec 2021 23:50:03: 22000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:50:06: 26000000 INFO @ Wed, 08 Dec 2021 23:50:11: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 23:50:11: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 23:50:11: #1 total tags in treatment: 11744783 INFO @ Wed, 08 Dec 2021 23:50:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:50:11: #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 23:50:11: 23000000 INFO @ Wed, 08 Dec 2021 23:50:11: #1 tags after filtering in treatment: 9539163 INFO @ Wed, 08 Dec 2021 23:50:11: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 23:50:11: #1 finished! INFO @ Wed, 08 Dec 2021 23:50:11: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:50:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:50:12: #2 number of paired peaks: 3899 INFO @ Wed, 08 Dec 2021 23:50:12: start model_add_line... INFO @ Wed, 08 Dec 2021 23:50:12: start X-correlation... INFO @ Wed, 08 Dec 2021 23:50:12: end of X-cor INFO @ Wed, 08 Dec 2021 23:50:12: #2 finished! INFO @ Wed, 08 Dec 2021 23:50:12: #2 predicted fragment length is 257 bps INFO @ Wed, 08 Dec 2021 23:50:12: #2 alternative fragment length(s) may be 2,257 bps INFO @ Wed, 08 Dec 2021 23:50:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.10_model.r INFO @ Wed, 08 Dec 2021 23:50:12: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:50:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:50:19: 24000000 INFO @ Wed, 08 Dec 2021 23:50:27: 25000000 INFO @ Wed, 08 Dec 2021 23:50:35: 26000000 INFO @ Wed, 08 Dec 2021 23:50:40: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 23:50:40: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 23:50:40: #1 total tags in treatment: 11744783 INFO @ Wed, 08 Dec 2021 23:50:40: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:50:40: #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 23:50:40: #1 tags after filtering in treatment: 9539163 INFO @ Wed, 08 Dec 2021 23:50:40: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 23:50:40: #1 finished! INFO @ Wed, 08 Dec 2021 23:50:40: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:50:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:50:41: #2 number of paired peaks: 3899 INFO @ Wed, 08 Dec 2021 23:50:41: start model_add_line... INFO @ Wed, 08 Dec 2021 23:50:41: start X-correlation... INFO @ Wed, 08 Dec 2021 23:50:41: end of X-cor INFO @ Wed, 08 Dec 2021 23:50:41: #2 finished! INFO @ Wed, 08 Dec 2021 23:50:41: #2 predicted fragment length is 257 bps INFO @ Wed, 08 Dec 2021 23:50:41: #2 alternative fragment length(s) may be 2,257 bps INFO @ Wed, 08 Dec 2021 23:50:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.20_model.r INFO @ Wed, 08 Dec 2021 23:50:41: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:50:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:50:51: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:51:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:51:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:51:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.10_summits.bed INFO @ Wed, 08 Dec 2021 23:51:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (726 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:51:19: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:51:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:51:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:51:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976689/SRX8976689.20_summits.bed INFO @ Wed, 08 Dec 2021 23:51:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (302 records, 4 fields): 2 millis CompletedMACS2peakCalling