Job ID = 14158151 SRX = SRX10342574 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15995252 spots for SRR13964604/SRR13964604.sra Written 15995252 spots for SRR13964604/SRR13964604.sra Read 15999228 spots for SRR13964605/SRR13964605.sra Written 15999228 spots for SRR13964605/SRR13964605.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158787 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:03:29 31994480 reads; of these: 31994480 (100.00%) were paired; of these: 10305722 (32.21%) aligned concordantly 0 times 12205719 (38.15%) aligned concordantly exactly 1 time 9483039 (29.64%) aligned concordantly >1 times ---- 10305722 pairs aligned concordantly 0 times; of these: 2359669 (22.90%) aligned discordantly 1 time ---- 7946053 pairs aligned 0 times concordantly or discordantly; of these: 15892106 mates make up the pairs; of these: 12333358 (77.61%) aligned 0 times 1469391 (9.25%) aligned exactly 1 time 2089357 (13.15%) aligned >1 times 80.73% overall alignment rate Time searching: 01:03:30 Overall time: 01:03:30 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 24 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] 8161892 / 23945990 = 0.3408 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 15:55:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.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 15:55:27: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:55:27: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:55:33: 1000000 INFO @ Wed, 08 Dec 2021 15:55:40: 2000000 INFO @ Wed, 08 Dec 2021 15:55:46: 3000000 INFO @ Wed, 08 Dec 2021 15:55:52: 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 15:55:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.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 15:55:57: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:55:57: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:55:58: 5000000 INFO @ Wed, 08 Dec 2021 15:56:04: 6000000 INFO @ Wed, 08 Dec 2021 15:56:06: 1000000 INFO @ Wed, 08 Dec 2021 15:56:10: 7000000 INFO @ Wed, 08 Dec 2021 15:56:15: 2000000 INFO @ Wed, 08 Dec 2021 15:56:16: 8000000 INFO @ Wed, 08 Dec 2021 15:56:22: 9000000 BedGraph に変換中... INFO @ Wed, 08 Dec 2021 15:56:24: 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 15:56:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.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 15:56:27: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:56:27: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:56:29: 10000000 INFO @ Wed, 08 Dec 2021 15:56:33: 4000000 INFO @ Wed, 08 Dec 2021 15:56:34: 1000000 INFO @ Wed, 08 Dec 2021 15:56:35: 11000000 INFO @ Wed, 08 Dec 2021 15:56:41: 2000000 INFO @ Wed, 08 Dec 2021 15:56:42: 12000000 INFO @ Wed, 08 Dec 2021 15:56:42: 5000000 INFO @ Wed, 08 Dec 2021 15:56:47: 3000000 INFO @ Wed, 08 Dec 2021 15:56:48: 13000000 INFO @ Wed, 08 Dec 2021 15:56:50: 6000000 INFO @ Wed, 08 Dec 2021 15:56:53: 4000000 INFO @ Wed, 08 Dec 2021 15:56:54: 14000000 INFO @ Wed, 08 Dec 2021 15:56:59: 7000000 INFO @ Wed, 08 Dec 2021 15:57:00: 5000000 INFO @ Wed, 08 Dec 2021 15:57:00: 15000000 INFO @ Wed, 08 Dec 2021 15:57:06: 6000000 INFO @ Wed, 08 Dec 2021 15:57:06: 16000000 INFO @ Wed, 08 Dec 2021 15:57:08: 8000000 INFO @ Wed, 08 Dec 2021 15:57:12: 7000000 INFO @ Wed, 08 Dec 2021 15:57:12: 17000000 INFO @ Wed, 08 Dec 2021 15:57:17: 9000000 INFO @ Wed, 08 Dec 2021 15:57:18: 8000000 INFO @ Wed, 08 Dec 2021 15:57:19: 18000000 INFO @ Wed, 08 Dec 2021 15:57:24: 10000000 INFO @ Wed, 08 Dec 2021 15:57:24: 9000000 INFO @ Wed, 08 Dec 2021 15:57:25: 19000000 INFO @ Wed, 08 Dec 2021 15:57:31: 10000000 INFO @ Wed, 08 Dec 2021 15:57:31: 20000000 INFO @ Wed, 08 Dec 2021 15:57:33: 11000000 INFO @ Wed, 08 Dec 2021 15:57:37: 11000000 INFO @ Wed, 08 Dec 2021 15:57:38: 21000000 INFO @ Wed, 08 Dec 2021 15:57:40: 12000000 INFO @ Wed, 08 Dec 2021 15:57:43: 12000000 INFO @ Wed, 08 Dec 2021 15:57:45: 22000000 INFO @ Wed, 08 Dec 2021 15:57:48: 13000000 INFO @ Wed, 08 Dec 2021 15:57:49: 13000000 INFO @ Wed, 08 Dec 2021 15:57:51: 23000000 INFO @ Wed, 08 Dec 2021 15:57:56: 14000000 INFO @ Wed, 08 Dec 2021 15:57:56: 14000000 INFO @ Wed, 08 Dec 2021 15:57:57: 24000000 INFO @ Wed, 08 Dec 2021 15:58:02: 15000000 INFO @ Wed, 08 Dec 2021 15:58:03: 25000000 INFO @ Wed, 08 Dec 2021 15:58:05: 15000000 INFO @ Wed, 08 Dec 2021 15:58:08: 16000000 INFO @ Wed, 08 Dec 2021 15:58:09: 26000000 INFO @ Wed, 08 Dec 2021 15:58:13: 16000000 INFO @ Wed, 08 Dec 2021 15:58:14: 17000000 INFO @ Wed, 08 Dec 2021 15:58:15: 27000000 INFO @ Wed, 08 Dec 2021 15:58:20: 18000000 INFO @ Wed, 08 Dec 2021 15:58:21: 28000000 INFO @ Wed, 08 Dec 2021 15:58:22: 17000000 INFO @ Wed, 08 Dec 2021 15:58:27: 19000000 INFO @ Wed, 08 Dec 2021 15:58:28: 29000000 INFO @ Wed, 08 Dec 2021 15:58:30: 18000000 INFO @ Wed, 08 Dec 2021 15:58:33: 20000000 INFO @ Wed, 08 Dec 2021 15:58:34: 30000000 INFO @ Wed, 08 Dec 2021 15:58:38: 19000000 INFO @ Wed, 08 Dec 2021 15:58:40: 31000000 INFO @ Wed, 08 Dec 2021 15:58:40: 21000000 INFO @ Wed, 08 Dec 2021 15:58:46: 32000000 INFO @ Wed, 08 Dec 2021 15:58:46: 20000000 INFO @ Wed, 08 Dec 2021 15:58:47: 22000000 INFO @ Wed, 08 Dec 2021 15:58:52: 33000000 INFO @ Wed, 08 Dec 2021 15:58:53: 23000000 INFO @ Wed, 08 Dec 2021 15:58:56: 21000000 INFO @ Wed, 08 Dec 2021 15:58:58: 34000000 INFO @ Wed, 08 Dec 2021 15:58:59: 24000000 INFO @ Wed, 08 Dec 2021 15:59:04: 35000000 INFO @ Wed, 08 Dec 2021 15:59:04: 22000000 INFO @ Wed, 08 Dec 2021 15:59:05: 25000000 INFO @ Wed, 08 Dec 2021 15:59:06: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 15:59:06: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 15:59:06: #1 total tags in treatment: 14039390 INFO @ Wed, 08 Dec 2021 15:59:06: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:59:06: #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 15:59:06: #1 tags after filtering in treatment: 8626658 INFO @ Wed, 08 Dec 2021 15:59:06: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 08 Dec 2021 15:59:06: #1 finished! INFO @ Wed, 08 Dec 2021 15:59:06: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:59:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:59:07: #2 number of paired peaks: 2248 INFO @ Wed, 08 Dec 2021 15:59:07: start model_add_line... INFO @ Wed, 08 Dec 2021 15:59:08: start X-correlation... INFO @ Wed, 08 Dec 2021 15:59:08: end of X-cor INFO @ Wed, 08 Dec 2021 15:59:08: #2 finished! INFO @ Wed, 08 Dec 2021 15:59:08: #2 predicted fragment length is 219 bps INFO @ Wed, 08 Dec 2021 15:59:08: #2 alternative fragment length(s) may be 219 bps INFO @ Wed, 08 Dec 2021 15:59:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.05_model.r INFO @ Wed, 08 Dec 2021 15:59:08: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:59:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:59:11: 26000000 INFO @ Wed, 08 Dec 2021 15:59:12: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:59:17: 27000000 INFO @ Wed, 08 Dec 2021 15:59:20: 24000000 INFO @ Wed, 08 Dec 2021 15:59:23: 28000000 INFO @ Wed, 08 Dec 2021 15:59:28: 25000000 INFO @ Wed, 08 Dec 2021 15:59:29: 29000000 INFO @ Wed, 08 Dec 2021 15:59:35: 30000000 INFO @ Wed, 08 Dec 2021 15:59:35: 26000000 INFO @ Wed, 08 Dec 2021 15:59:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:59:41: 31000000 INFO @ Wed, 08 Dec 2021 15:59:44: 27000000 INFO @ Wed, 08 Dec 2021 15:59:47: 32000000 INFO @ Wed, 08 Dec 2021 15:59:52: 28000000 INFO @ Wed, 08 Dec 2021 15:59:53: 33000000 INFO @ Wed, 08 Dec 2021 15:59:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:59:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:59:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.05_summits.bed INFO @ Wed, 08 Dec 2021 15:59:54: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (15194 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:59:59: 34000000 INFO @ Wed, 08 Dec 2021 16:00:00: 29000000 INFO @ Wed, 08 Dec 2021 16:00:05: 35000000 INFO @ Wed, 08 Dec 2021 16:00:07: 30000000 INFO @ Wed, 08 Dec 2021 16:00:08: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 16:00:08: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 16:00:08: #1 total tags in treatment: 14039390 INFO @ Wed, 08 Dec 2021 16:00:08: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:00:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 16:00:08: #1 tags after filtering in treatment: 8626658 INFO @ Wed, 08 Dec 2021 16:00:08: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 08 Dec 2021 16:00:08: #1 finished! INFO @ Wed, 08 Dec 2021 16:00:08: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:00:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:00:09: #2 number of paired peaks: 2248 INFO @ Wed, 08 Dec 2021 16:00:09: start model_add_line... INFO @ Wed, 08 Dec 2021 16:00:09: start X-correlation... INFO @ Wed, 08 Dec 2021 16:00:09: end of X-cor INFO @ Wed, 08 Dec 2021 16:00:09: #2 finished! INFO @ Wed, 08 Dec 2021 16:00:09: #2 predicted fragment length is 219 bps INFO @ Wed, 08 Dec 2021 16:00:09: #2 alternative fragment length(s) may be 219 bps INFO @ Wed, 08 Dec 2021 16:00:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.20_model.r INFO @ Wed, 08 Dec 2021 16:00:09: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:00:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:00:15: 31000000 INFO @ Wed, 08 Dec 2021 16:00:22: 32000000 INFO @ Wed, 08 Dec 2021 16:00:30: 33000000 INFO @ Wed, 08 Dec 2021 16:00:38: 34000000 INFO @ Wed, 08 Dec 2021 16:00:42: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:00:46: 35000000 INFO @ Wed, 08 Dec 2021 16:00:48: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 16:00:48: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 16:00:48: #1 total tags in treatment: 14039390 INFO @ Wed, 08 Dec 2021 16:00:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:00:48: #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 16:00:49: #1 tags after filtering in treatment: 8626658 INFO @ Wed, 08 Dec 2021 16:00:49: #1 Redundant rate of treatment: 0.39 INFO @ Wed, 08 Dec 2021 16:00:49: #1 finished! INFO @ Wed, 08 Dec 2021 16:00:49: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:00:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:00:50: #2 number of paired peaks: 2248 INFO @ Wed, 08 Dec 2021 16:00:50: start model_add_line... INFO @ Wed, 08 Dec 2021 16:00:50: start X-correlation... INFO @ Wed, 08 Dec 2021 16:00:50: end of X-cor INFO @ Wed, 08 Dec 2021 16:00:50: #2 finished! INFO @ Wed, 08 Dec 2021 16:00:50: #2 predicted fragment length is 219 bps INFO @ Wed, 08 Dec 2021 16:00:50: #2 alternative fragment length(s) may be 219 bps INFO @ Wed, 08 Dec 2021 16:00:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.10_model.r INFO @ Wed, 08 Dec 2021 16:00:50: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:00:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:00:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:00:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:00:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.20_summits.bed INFO @ Wed, 08 Dec 2021 16:00:55: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2619 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:01:23: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:01:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:01:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:01:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342574/SRX10342574.10_summits.bed INFO @ Wed, 08 Dec 2021 16:01:37: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7844 records, 4 fields): 12 millis CompletedMACS2peakCalling