Job ID = 14158667 SRX = SRX10342570 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: 00:36:15 19316820 reads; of these: 19316820 (100.00%) were paired; of these: 5983108 (30.97%) aligned concordantly 0 times 5102226 (26.41%) aligned concordantly exactly 1 time 8231486 (42.61%) aligned concordantly >1 times ---- 5983108 pairs aligned concordantly 0 times; of these: 917362 (15.33%) aligned discordantly 1 time ---- 5065746 pairs aligned 0 times concordantly or discordantly; of these: 10131492 mates make up the pairs; of these: 6936967 (68.47%) aligned 0 times 2025757 (19.99%) aligned exactly 1 time 1168768 (11.54%) aligned >1 times 82.04% overall alignment rate Time searching: 00:36:15 Overall time: 00:36:15 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] 2691999 / 13793862 = 0.1952 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 18:25:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.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 18:25:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:25:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:25:22: 1000000 INFO @ Wed, 08 Dec 2021 18:25:27: 2000000 INFO @ Wed, 08 Dec 2021 18:25:31: 3000000 INFO @ Wed, 08 Dec 2021 18:25:35: 4000000 INFO @ Wed, 08 Dec 2021 18:25:39: 5000000 INFO @ Wed, 08 Dec 2021 18:25:43: 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 18:25:47: 7000000 INFO @ Wed, 08 Dec 2021 18:25:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.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 18:25:48: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:25:48: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:25:52: 8000000 INFO @ Wed, 08 Dec 2021 18:25:53: 1000000 INFO @ Wed, 08 Dec 2021 18:25:56: 9000000 INFO @ Wed, 08 Dec 2021 18:25:58: 2000000 INFO @ Wed, 08 Dec 2021 18:26:00: 10000000 INFO @ Wed, 08 Dec 2021 18:26:04: 3000000 INFO @ Wed, 08 Dec 2021 18:26:04: 11000000 INFO @ Wed, 08 Dec 2021 18:26:09: 4000000 INFO @ Wed, 08 Dec 2021 18:26:09: 12000000 INFO @ Wed, 08 Dec 2021 18:26:13: 13000000 INFO @ Wed, 08 Dec 2021 18:26:14: 5000000 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 18:26:17: 14000000 INFO @ Wed, 08 Dec 2021 18:26:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.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 18:26:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:26:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:26:19: 6000000 INFO @ Wed, 08 Dec 2021 18:26:22: 15000000 INFO @ Wed, 08 Dec 2021 18:26:23: 1000000 INFO @ Wed, 08 Dec 2021 18:26:24: 7000000 INFO @ Wed, 08 Dec 2021 18:26:26: 16000000 INFO @ Wed, 08 Dec 2021 18:26:27: 2000000 INFO @ Wed, 08 Dec 2021 18:26:29: 8000000 INFO @ Wed, 08 Dec 2021 18:26:31: 17000000 INFO @ Wed, 08 Dec 2021 18:26:31: 3000000 INFO @ Wed, 08 Dec 2021 18:26:34: 9000000 INFO @ Wed, 08 Dec 2021 18:26:35: 18000000 INFO @ Wed, 08 Dec 2021 18:26:36: 4000000 INFO @ Wed, 08 Dec 2021 18:26:39: 19000000 INFO @ Wed, 08 Dec 2021 18:26:40: 10000000 INFO @ Wed, 08 Dec 2021 18:26:40: 5000000 INFO @ Wed, 08 Dec 2021 18:26:44: 20000000 INFO @ Wed, 08 Dec 2021 18:26:45: 6000000 INFO @ Wed, 08 Dec 2021 18:26:45: 11000000 INFO @ Wed, 08 Dec 2021 18:26:48: 21000000 INFO @ Wed, 08 Dec 2021 18:26:49: 7000000 INFO @ Wed, 08 Dec 2021 18:26:50: 12000000 INFO @ Wed, 08 Dec 2021 18:26:52: 22000000 INFO @ Wed, 08 Dec 2021 18:26:53: 8000000 INFO @ Wed, 08 Dec 2021 18:26:55: 13000000 INFO @ Wed, 08 Dec 2021 18:26:57: 23000000 INFO @ Wed, 08 Dec 2021 18:26:58: 9000000 INFO @ Wed, 08 Dec 2021 18:27:01: 14000000 INFO @ Wed, 08 Dec 2021 18:27:01: 24000000 INFO @ Wed, 08 Dec 2021 18:27:02: 10000000 INFO @ Wed, 08 Dec 2021 18:27:05: 25000000 INFO @ Wed, 08 Dec 2021 18:27:06: 15000000 INFO @ Wed, 08 Dec 2021 18:27:06: 11000000 INFO @ Wed, 08 Dec 2021 18:27:09: 26000000 INFO @ Wed, 08 Dec 2021 18:27:11: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:27:11: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:27:11: #1 total tags in treatment: 10690018 INFO @ Wed, 08 Dec 2021 18:27:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:27:11: #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 18:27:11: 12000000 INFO @ Wed, 08 Dec 2021 18:27:11: #1 tags after filtering in treatment: 4770753 INFO @ Wed, 08 Dec 2021 18:27:11: #1 Redundant rate of treatment: 0.55 INFO @ Wed, 08 Dec 2021 18:27:11: #1 finished! INFO @ Wed, 08 Dec 2021 18:27:11: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:27:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:27:11: 16000000 INFO @ Wed, 08 Dec 2021 18:27:11: #2 number of paired peaks: 2367 INFO @ Wed, 08 Dec 2021 18:27:11: start model_add_line... INFO @ Wed, 08 Dec 2021 18:27:12: start X-correlation... INFO @ Wed, 08 Dec 2021 18:27:12: end of X-cor INFO @ Wed, 08 Dec 2021 18:27:12: #2 finished! INFO @ Wed, 08 Dec 2021 18:27:12: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 18:27:12: #2 alternative fragment length(s) may be 4,157 bps INFO @ Wed, 08 Dec 2021 18:27:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.05_model.r INFO @ Wed, 08 Dec 2021 18:27:12: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:27:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:27:15: 13000000 INFO @ Wed, 08 Dec 2021 18:27:17: 17000000 INFO @ Wed, 08 Dec 2021 18:27:20: 14000000 INFO @ Wed, 08 Dec 2021 18:27:22: 18000000 INFO @ Wed, 08 Dec 2021 18:27:24: 15000000 INFO @ Wed, 08 Dec 2021 18:27:25: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:27:27: 19000000 INFO @ Wed, 08 Dec 2021 18:27:28: 16000000 INFO @ Wed, 08 Dec 2021 18:27:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:27:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:27:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.05_summits.bed INFO @ Wed, 08 Dec 2021 18:27:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3321 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:27:32: 20000000 INFO @ Wed, 08 Dec 2021 18:27:33: 17000000 INFO @ Wed, 08 Dec 2021 18:27:37: 18000000 INFO @ Wed, 08 Dec 2021 18:27:38: 21000000 INFO @ Wed, 08 Dec 2021 18:27:41: 19000000 INFO @ Wed, 08 Dec 2021 18:27:43: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:27:46: 20000000 INFO @ Wed, 08 Dec 2021 18:27:48: 23000000 INFO @ Wed, 08 Dec 2021 18:27:50: 21000000 INFO @ Wed, 08 Dec 2021 18:27:53: 24000000 INFO @ Wed, 08 Dec 2021 18:27:55: 22000000 INFO @ Wed, 08 Dec 2021 18:27:58: 25000000 INFO @ Wed, 08 Dec 2021 18:27:59: 23000000 INFO @ Wed, 08 Dec 2021 18:28:03: 24000000 INFO @ Wed, 08 Dec 2021 18:28:03: 26000000 INFO @ Wed, 08 Dec 2021 18:28:05: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:28:05: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:28:05: #1 total tags in treatment: 10690018 INFO @ Wed, 08 Dec 2021 18:28:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:28:05: #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 18:28:05: #1 tags after filtering in treatment: 4770753 INFO @ Wed, 08 Dec 2021 18:28:05: #1 Redundant rate of treatment: 0.55 INFO @ Wed, 08 Dec 2021 18:28:05: #1 finished! INFO @ Wed, 08 Dec 2021 18:28:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:28:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:28:06: #2 number of paired peaks: 2367 INFO @ Wed, 08 Dec 2021 18:28:06: start model_add_line... INFO @ Wed, 08 Dec 2021 18:28:06: start X-correlation... INFO @ Wed, 08 Dec 2021 18:28:06: end of X-cor INFO @ Wed, 08 Dec 2021 18:28:06: #2 finished! INFO @ Wed, 08 Dec 2021 18:28:06: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 18:28:06: #2 alternative fragment length(s) may be 4,157 bps INFO @ Wed, 08 Dec 2021 18:28:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.10_model.r INFO @ Wed, 08 Dec 2021 18:28:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:28:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:28:07: 25000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:28:11: 26000000 INFO @ Wed, 08 Dec 2021 18:28:13: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:28:13: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:28:13: #1 total tags in treatment: 10690018 INFO @ Wed, 08 Dec 2021 18:28:13: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:28:13: #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 18:28:13: #1 tags after filtering in treatment: 4770753 INFO @ Wed, 08 Dec 2021 18:28:13: #1 Redundant rate of treatment: 0.55 INFO @ Wed, 08 Dec 2021 18:28:13: #1 finished! INFO @ Wed, 08 Dec 2021 18:28:13: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:28:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:28:13: #2 number of paired peaks: 2367 INFO @ Wed, 08 Dec 2021 18:28:13: start model_add_line... INFO @ Wed, 08 Dec 2021 18:28:13: start X-correlation... INFO @ Wed, 08 Dec 2021 18:28:13: end of X-cor INFO @ Wed, 08 Dec 2021 18:28:13: #2 finished! INFO @ Wed, 08 Dec 2021 18:28:13: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 18:28:13: #2 alternative fragment length(s) may be 4,157 bps INFO @ Wed, 08 Dec 2021 18:28:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.20_model.r INFO @ Wed, 08 Dec 2021 18:28:13: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:28:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:28:19: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:28:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:28:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:28:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.10_summits.bed INFO @ Wed, 08 Dec 2021 18:28:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1977 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:28:27: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342570/SRX10342570.20_summits.bed INFO @ Wed, 08 Dec 2021 18:28:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1211 records, 4 fields): 3 millis CompletedMACS2peakCalling