Job ID = 14159614 SRX = SRX8976688 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: 00:15:12 16436153 reads; of these: 16436153 (100.00%) were paired; of these: 1904640 (11.59%) aligned concordantly 0 times 11306861 (68.79%) aligned concordantly exactly 1 time 3224652 (19.62%) aligned concordantly >1 times ---- 1904640 pairs aligned concordantly 0 times; of these: 1137787 (59.74%) aligned discordantly 1 time ---- 766853 pairs aligned 0 times concordantly or discordantly; of these: 1533706 mates make up the pairs; of these: 487418 (31.78%) aligned 0 times 375095 (24.46%) aligned exactly 1 time 671193 (43.76%) aligned >1 times 98.52% overall alignment rate Time searching: 00:15:12 Overall time: 00:15:12 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] 1327094 / 15656777 = 0.0848 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 23:42:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.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 23:42:54: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:42:54: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:43:00: 1000000 INFO @ Wed, 08 Dec 2021 23:43:06: 2000000 INFO @ Wed, 08 Dec 2021 23:43:12: 3000000 INFO @ Wed, 08 Dec 2021 23:43:18: 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 23:43:23: 5000000 INFO @ Wed, 08 Dec 2021 23:43:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.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 23:43:24: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:43:24: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:43:30: 6000000 INFO @ Wed, 08 Dec 2021 23:43:30: 1000000 INFO @ Wed, 08 Dec 2021 23:43:36: 7000000 INFO @ Wed, 08 Dec 2021 23:43:36: 2000000 INFO @ Wed, 08 Dec 2021 23:43:42: 3000000 INFO @ Wed, 08 Dec 2021 23:43:42: 8000000 INFO @ Wed, 08 Dec 2021 23:43:48: 4000000 INFO @ Wed, 08 Dec 2021 23:43:49: 9000000 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 23:43:54: 5000000 INFO @ Wed, 08 Dec 2021 23:43:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.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 23:43:54: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:43:54: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:43:55: 10000000 INFO @ Wed, 08 Dec 2021 23:44:00: 6000000 INFO @ Wed, 08 Dec 2021 23:44:01: 1000000 INFO @ Wed, 08 Dec 2021 23:44:02: 11000000 INFO @ Wed, 08 Dec 2021 23:44:06: 7000000 INFO @ Wed, 08 Dec 2021 23:44:08: 12000000 INFO @ Wed, 08 Dec 2021 23:44:08: 2000000 INFO @ Wed, 08 Dec 2021 23:44:12: 8000000 INFO @ Wed, 08 Dec 2021 23:44:14: 13000000 INFO @ Wed, 08 Dec 2021 23:44:15: 3000000 INFO @ Wed, 08 Dec 2021 23:44:18: 9000000 INFO @ Wed, 08 Dec 2021 23:44:21: 14000000 INFO @ Wed, 08 Dec 2021 23:44:22: 4000000 INFO @ Wed, 08 Dec 2021 23:44:24: 10000000 INFO @ Wed, 08 Dec 2021 23:44:27: 15000000 INFO @ Wed, 08 Dec 2021 23:44:29: 5000000 INFO @ Wed, 08 Dec 2021 23:44:29: 11000000 INFO @ Wed, 08 Dec 2021 23:44:34: 16000000 INFO @ Wed, 08 Dec 2021 23:44:35: 6000000 INFO @ Wed, 08 Dec 2021 23:44:36: 12000000 INFO @ Wed, 08 Dec 2021 23:44:40: 17000000 INFO @ Wed, 08 Dec 2021 23:44:41: 13000000 INFO @ Wed, 08 Dec 2021 23:44:42: 7000000 INFO @ Wed, 08 Dec 2021 23:44:47: 18000000 INFO @ Wed, 08 Dec 2021 23:44:47: 14000000 INFO @ Wed, 08 Dec 2021 23:44:49: 8000000 INFO @ Wed, 08 Dec 2021 23:44:53: 19000000 INFO @ Wed, 08 Dec 2021 23:44:53: 15000000 INFO @ Wed, 08 Dec 2021 23:44:56: 9000000 INFO @ Wed, 08 Dec 2021 23:44:59: 16000000 INFO @ Wed, 08 Dec 2021 23:45:00: 20000000 INFO @ Wed, 08 Dec 2021 23:45:03: 10000000 INFO @ Wed, 08 Dec 2021 23:45:05: 17000000 INFO @ Wed, 08 Dec 2021 23:45:06: 21000000 INFO @ Wed, 08 Dec 2021 23:45:10: 11000000 INFO @ Wed, 08 Dec 2021 23:45:11: 18000000 INFO @ Wed, 08 Dec 2021 23:45:12: 22000000 INFO @ Wed, 08 Dec 2021 23:45:17: 12000000 INFO @ Wed, 08 Dec 2021 23:45:17: 19000000 INFO @ Wed, 08 Dec 2021 23:45:19: 23000000 INFO @ Wed, 08 Dec 2021 23:45:23: 20000000 INFO @ Wed, 08 Dec 2021 23:45:23: 13000000 INFO @ Wed, 08 Dec 2021 23:45:25: 24000000 INFO @ Wed, 08 Dec 2021 23:45:29: 21000000 INFO @ Wed, 08 Dec 2021 23:45:30: 14000000 INFO @ Wed, 08 Dec 2021 23:45:32: 25000000 INFO @ Wed, 08 Dec 2021 23:45:35: 22000000 INFO @ Wed, 08 Dec 2021 23:45:37: 15000000 INFO @ Wed, 08 Dec 2021 23:45:38: 26000000 INFO @ Wed, 08 Dec 2021 23:45:41: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:45:44: 16000000 INFO @ Wed, 08 Dec 2021 23:45:44: 27000000 INFO @ Wed, 08 Dec 2021 23:45:47: 24000000 INFO @ Wed, 08 Dec 2021 23:45:51: 17000000 INFO @ Wed, 08 Dec 2021 23:45:51: 28000000 INFO @ Wed, 08 Dec 2021 23:45:53: 25000000 INFO @ Wed, 08 Dec 2021 23:45:57: 29000000 INFO @ Wed, 08 Dec 2021 23:45:58: 18000000 INFO @ Wed, 08 Dec 2021 23:45:59: 26000000 INFO @ Wed, 08 Dec 2021 23:46:02: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 23:46:02: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 23:46:02: #1 total tags in treatment: 13271897 INFO @ Wed, 08 Dec 2021 23:46:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:46:02: #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 23:46:02: #1 tags after filtering in treatment: 11335301 INFO @ Wed, 08 Dec 2021 23:46:02: #1 Redundant rate of treatment: 0.15 INFO @ Wed, 08 Dec 2021 23:46:02: #1 finished! INFO @ Wed, 08 Dec 2021 23:46:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:46:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:46:03: #2 number of paired peaks: 1347 INFO @ Wed, 08 Dec 2021 23:46:03: start model_add_line... INFO @ Wed, 08 Dec 2021 23:46:03: start X-correlation... INFO @ Wed, 08 Dec 2021 23:46:03: end of X-cor INFO @ Wed, 08 Dec 2021 23:46:03: #2 finished! INFO @ Wed, 08 Dec 2021 23:46:03: #2 predicted fragment length is 193 bps INFO @ Wed, 08 Dec 2021 23:46:03: #2 alternative fragment length(s) may be 2,136,175,178,193 bps INFO @ Wed, 08 Dec 2021 23:46:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.05_model.r INFO @ Wed, 08 Dec 2021 23:46:03: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:46:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:46:04: 27000000 INFO @ Wed, 08 Dec 2021 23:46:05: 19000000 INFO @ Wed, 08 Dec 2021 23:46:10: 28000000 INFO @ Wed, 08 Dec 2021 23:46:11: 20000000 INFO @ Wed, 08 Dec 2021 23:46:16: 29000000 INFO @ Wed, 08 Dec 2021 23:46:18: 21000000 INFO @ Wed, 08 Dec 2021 23:46:20: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 23:46:20: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 23:46:20: #1 total tags in treatment: 13271897 INFO @ Wed, 08 Dec 2021 23:46:20: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:46:20: #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 23:46:21: #1 tags after filtering in treatment: 11335301 INFO @ Wed, 08 Dec 2021 23:46:21: #1 Redundant rate of treatment: 0.15 INFO @ Wed, 08 Dec 2021 23:46:21: #1 finished! INFO @ Wed, 08 Dec 2021 23:46:21: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:46:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:46:21: #2 number of paired peaks: 1347 INFO @ Wed, 08 Dec 2021 23:46:21: start model_add_line... INFO @ Wed, 08 Dec 2021 23:46:22: start X-correlation... INFO @ Wed, 08 Dec 2021 23:46:22: end of X-cor INFO @ Wed, 08 Dec 2021 23:46:22: #2 finished! INFO @ Wed, 08 Dec 2021 23:46:22: #2 predicted fragment length is 193 bps INFO @ Wed, 08 Dec 2021 23:46:22: #2 alternative fragment length(s) may be 2,136,175,178,193 bps INFO @ Wed, 08 Dec 2021 23:46:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.10_model.r INFO @ Wed, 08 Dec 2021 23:46:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:46:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:46:25: 22000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:46:31: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:46:31: 23000000 INFO @ Wed, 08 Dec 2021 23:46:37: 24000000 INFO @ Wed, 08 Dec 2021 23:46:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:46:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:46:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.05_summits.bed INFO @ Wed, 08 Dec 2021 23:46:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (871 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:46:43: 25000000 INFO @ Wed, 08 Dec 2021 23:46:49: 26000000 INFO @ Wed, 08 Dec 2021 23:46:50: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:46:55: 27000000 INFO @ Wed, 08 Dec 2021 23:47:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:47:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:47:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.10_summits.bed INFO @ Wed, 08 Dec 2021 23:47:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (405 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:47:01: 28000000 INFO @ Wed, 08 Dec 2021 23:47:07: 29000000 INFO @ Wed, 08 Dec 2021 23:47:12: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 23:47:12: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 23:47:12: #1 total tags in treatment: 13271897 INFO @ Wed, 08 Dec 2021 23:47:12: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:47:12: #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 23:47:12: #1 tags after filtering in treatment: 11335301 INFO @ Wed, 08 Dec 2021 23:47:12: #1 Redundant rate of treatment: 0.15 INFO @ Wed, 08 Dec 2021 23:47:12: #1 finished! INFO @ Wed, 08 Dec 2021 23:47:12: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:47:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:47:13: #2 number of paired peaks: 1347 INFO @ Wed, 08 Dec 2021 23:47:13: start model_add_line... INFO @ Wed, 08 Dec 2021 23:47:13: start X-correlation... INFO @ Wed, 08 Dec 2021 23:47:13: end of X-cor INFO @ Wed, 08 Dec 2021 23:47:13: #2 finished! INFO @ Wed, 08 Dec 2021 23:47:13: #2 predicted fragment length is 193 bps INFO @ Wed, 08 Dec 2021 23:47:13: #2 alternative fragment length(s) may be 2,136,175,178,193 bps INFO @ Wed, 08 Dec 2021 23:47:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.20_model.r INFO @ Wed, 08 Dec 2021 23:47:13: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:47:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:47:39: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:47:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:47:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:47:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976688/SRX8976688.20_summits.bed INFO @ Wed, 08 Dec 2021 23:47:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (207 records, 4 fields): 1 millis CompletedMACS2peakCalling