Job ID = 14158250 SRX = SRX10342579 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9155990 spots for SRR13964614/SRR13964614.sra Written 9155990 spots for SRR13964614/SRR13964614.sra Read 10047890 spots for SRR13964615/SRR13964615.sra Written 10047890 spots for SRR13964615/SRR13964615.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158779 ("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: 00:18:31 19203880 reads; of these: 19203880 (100.00%) were paired; of these: 7040053 (36.66%) aligned concordantly 0 times 10194729 (53.09%) aligned concordantly exactly 1 time 1969098 (10.25%) aligned concordantly >1 times ---- 7040053 pairs aligned concordantly 0 times; of these: 4551707 (64.65%) aligned discordantly 1 time ---- 2488346 pairs aligned 0 times concordantly or discordantly; of these: 4976692 mates make up the pairs; of these: 3104888 (62.39%) aligned 0 times 737931 (14.83%) aligned exactly 1 time 1133873 (22.78%) aligned >1 times 91.92% overall alignment rate Time searching: 00:18:31 Overall time: 00:18:31 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] 4618640 / 16707284 = 0.2764 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 15:43:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.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 15:43:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:43:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:43:30: 1000000 INFO @ Wed, 08 Dec 2021 15:43:36: 2000000 INFO @ Wed, 08 Dec 2021 15:43:42: 3000000 INFO @ Wed, 08 Dec 2021 15:43:48: 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 15:43:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.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 15:43:53: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:43:53: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:43:54: 5000000 INFO @ Wed, 08 Dec 2021 15:43:59: 1000000 INFO @ Wed, 08 Dec 2021 15:44:00: 6000000 INFO @ Wed, 08 Dec 2021 15:44:05: 2000000 INFO @ Wed, 08 Dec 2021 15:44:06: 7000000 INFO @ Wed, 08 Dec 2021 15:44:11: 3000000 INFO @ Wed, 08 Dec 2021 15:44:12: 8000000 INFO @ Wed, 08 Dec 2021 15:44:17: 4000000 INFO @ Wed, 08 Dec 2021 15:44:19: 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 15:44:23: 5000000 INFO @ Wed, 08 Dec 2021 15:44:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.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 15:44:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:44:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:44:25: 10000000 INFO @ Wed, 08 Dec 2021 15:44:28: 6000000 INFO @ Wed, 08 Dec 2021 15:44:30: 1000000 INFO @ Wed, 08 Dec 2021 15:44:31: 11000000 INFO @ Wed, 08 Dec 2021 15:44:34: 7000000 INFO @ Wed, 08 Dec 2021 15:44:36: 2000000 INFO @ Wed, 08 Dec 2021 15:44:37: 12000000 INFO @ Wed, 08 Dec 2021 15:44:40: 8000000 INFO @ Wed, 08 Dec 2021 15:44:41: 3000000 INFO @ Wed, 08 Dec 2021 15:44:43: 13000000 INFO @ Wed, 08 Dec 2021 15:44:46: 9000000 INFO @ Wed, 08 Dec 2021 15:44:47: 4000000 INFO @ Wed, 08 Dec 2021 15:44:50: 14000000 INFO @ Wed, 08 Dec 2021 15:44:52: 10000000 INFO @ Wed, 08 Dec 2021 15:44:53: 5000000 INFO @ Wed, 08 Dec 2021 15:44:56: 15000000 INFO @ Wed, 08 Dec 2021 15:44:57: 11000000 INFO @ Wed, 08 Dec 2021 15:44:59: 6000000 INFO @ Wed, 08 Dec 2021 15:45:02: 16000000 INFO @ Wed, 08 Dec 2021 15:45:03: 12000000 INFO @ Wed, 08 Dec 2021 15:45:05: 7000000 INFO @ Wed, 08 Dec 2021 15:45:08: 17000000 INFO @ Wed, 08 Dec 2021 15:45:09: 13000000 INFO @ Wed, 08 Dec 2021 15:45:12: 8000000 INFO @ Wed, 08 Dec 2021 15:45:14: 18000000 INFO @ Wed, 08 Dec 2021 15:45:16: 14000000 INFO @ Wed, 08 Dec 2021 15:45:19: 9000000 INFO @ Wed, 08 Dec 2021 15:45:20: 19000000 INFO @ Wed, 08 Dec 2021 15:45:22: 15000000 INFO @ Wed, 08 Dec 2021 15:45:25: 10000000 INFO @ Wed, 08 Dec 2021 15:45:26: 20000000 INFO @ Wed, 08 Dec 2021 15:45:28: 16000000 INFO @ Wed, 08 Dec 2021 15:45:31: 11000000 INFO @ Wed, 08 Dec 2021 15:45:32: 21000000 INFO @ Wed, 08 Dec 2021 15:45:34: 17000000 INFO @ Wed, 08 Dec 2021 15:45:37: 12000000 INFO @ Wed, 08 Dec 2021 15:45:38: 22000000 INFO @ Wed, 08 Dec 2021 15:45:39: 18000000 INFO @ Wed, 08 Dec 2021 15:45:43: 13000000 INFO @ Wed, 08 Dec 2021 15:45:44: 23000000 INFO @ Wed, 08 Dec 2021 15:45:45: 19000000 INFO @ Wed, 08 Dec 2021 15:45:48: 14000000 INFO @ Wed, 08 Dec 2021 15:45:50: 20000000 INFO @ Wed, 08 Dec 2021 15:45:50: 24000000 INFO @ Wed, 08 Dec 2021 15:45:54: 15000000 INFO @ Wed, 08 Dec 2021 15:45:56: 21000000 INFO @ Wed, 08 Dec 2021 15:45:56: 25000000 INFO @ Wed, 08 Dec 2021 15:46:00: 16000000 INFO @ Wed, 08 Dec 2021 15:46:02: 22000000 INFO @ Wed, 08 Dec 2021 15:46:02: 26000000 INFO @ Wed, 08 Dec 2021 15:46:03: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:46:03: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:46:03: #1 total tags in treatment: 8584386 INFO @ Wed, 08 Dec 2021 15:46:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:46:03: #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 15:46:03: #1 tags after filtering in treatment: 7843362 INFO @ Wed, 08 Dec 2021 15:46:03: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 15:46:03: #1 finished! INFO @ Wed, 08 Dec 2021 15:46:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:46:04: #2 number of paired peaks: 665 WARNING @ Wed, 08 Dec 2021 15:46:04: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Wed, 08 Dec 2021 15:46:04: start model_add_line... INFO @ Wed, 08 Dec 2021 15:46:04: start X-correlation... INFO @ Wed, 08 Dec 2021 15:46:04: end of X-cor INFO @ Wed, 08 Dec 2021 15:46:04: #2 finished! INFO @ Wed, 08 Dec 2021 15:46:04: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 15:46:04: #2 alternative fragment length(s) may be 4,144 bps INFO @ Wed, 08 Dec 2021 15:46:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.05_model.r INFO @ Wed, 08 Dec 2021 15:46:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:46:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:46:05: 17000000 INFO @ Wed, 08 Dec 2021 15:46:07: 23000000 INFO @ Wed, 08 Dec 2021 15:46:11: 18000000 INFO @ Wed, 08 Dec 2021 15:46:13: 24000000 INFO @ Wed, 08 Dec 2021 15:46:17: 19000000 INFO @ Wed, 08 Dec 2021 15:46:18: 25000000 INFO @ Wed, 08 Dec 2021 15:46:22: 20000000 INFO @ Wed, 08 Dec 2021 15:46:24: 26000000 INFO @ Wed, 08 Dec 2021 15:46:24: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:46:24: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:46:24: #1 total tags in treatment: 8584386 INFO @ Wed, 08 Dec 2021 15:46:24: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:46:24: #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 15:46:25: #1 tags after filtering in treatment: 7843362 INFO @ Wed, 08 Dec 2021 15:46:25: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 15:46:25: #1 finished! INFO @ Wed, 08 Dec 2021 15:46:25: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:46:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:46:25: #2 number of paired peaks: 665 WARNING @ Wed, 08 Dec 2021 15:46:25: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Wed, 08 Dec 2021 15:46:25: start model_add_line... INFO @ Wed, 08 Dec 2021 15:46:25: start X-correlation... INFO @ Wed, 08 Dec 2021 15:46:26: end of X-cor INFO @ Wed, 08 Dec 2021 15:46:26: #2 finished! INFO @ Wed, 08 Dec 2021 15:46:26: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 15:46:26: #2 alternative fragment length(s) may be 4,144 bps INFO @ Wed, 08 Dec 2021 15:46:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.10_model.r INFO @ Wed, 08 Dec 2021 15:46:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:46:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:46:27: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:46:28: 21000000 INFO @ Wed, 08 Dec 2021 15:46:33: 22000000 INFO @ Wed, 08 Dec 2021 15:46:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:46:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:46:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.05_summits.bed INFO @ Wed, 08 Dec 2021 15:46:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (450 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:46:39: 23000000 INFO @ Wed, 08 Dec 2021 15:46:44: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:46:49: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:46:50: 25000000 INFO @ Wed, 08 Dec 2021 15:46:55: 26000000 INFO @ Wed, 08 Dec 2021 15:46:55: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:46:55: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:46:55: #1 total tags in treatment: 8584386 INFO @ Wed, 08 Dec 2021 15:46:55: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:46:55: #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 15:46:56: #1 tags after filtering in treatment: 7843362 INFO @ Wed, 08 Dec 2021 15:46:56: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 15:46:56: #1 finished! INFO @ Wed, 08 Dec 2021 15:46:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:46:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:46:56: #2 number of paired peaks: 665 WARNING @ Wed, 08 Dec 2021 15:46:56: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Wed, 08 Dec 2021 15:46:56: start model_add_line... INFO @ Wed, 08 Dec 2021 15:46:57: start X-correlation... INFO @ Wed, 08 Dec 2021 15:46:57: end of X-cor INFO @ Wed, 08 Dec 2021 15:46:57: #2 finished! INFO @ Wed, 08 Dec 2021 15:46:57: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 15:46:57: #2 alternative fragment length(s) may be 4,144 bps INFO @ Wed, 08 Dec 2021 15:46:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.20_model.r INFO @ Wed, 08 Dec 2021 15:46:57: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:46:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:47:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:47:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:47:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.10_summits.bed INFO @ Wed, 08 Dec 2021 15:47:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (344 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:47:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:47:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:47:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:47:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342579/SRX10342579.20_summits.bed INFO @ Wed, 08 Dec 2021 15:47:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (229 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。