Job ID = 14159087 SRX = SRX8976734 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14560532 spots for SRR12483278/SRR12483278.sra Written 14560532 spots for SRR12483278/SRR12483278.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159340 ("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: 00:11:07 14560532 reads; of these: 14560532 (100.00%) were paired; of these: 1045409 (7.18%) aligned concordantly 0 times 11762911 (80.79%) aligned concordantly exactly 1 time 1752212 (12.03%) aligned concordantly >1 times ---- 1045409 pairs aligned concordantly 0 times; of these: 746404 (71.40%) aligned discordantly 1 time ---- 299005 pairs aligned 0 times concordantly or discordantly; of these: 598010 mates make up the pairs; of these: 185934 (31.09%) aligned 0 times 195701 (32.73%) aligned exactly 1 time 216375 (36.18%) aligned >1 times 99.36% overall alignment rate Time searching: 00:11:07 Overall time: 00:11:07 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] 415462 / 14223656 = 0.0292 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 19:26:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.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 19:26:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:26:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:26:31: 1000000 INFO @ Wed, 08 Dec 2021 19:26:37: 2000000 INFO @ Wed, 08 Dec 2021 19:26:42: 3000000 INFO @ Wed, 08 Dec 2021 19:26:47: 4000000 INFO @ Wed, 08 Dec 2021 19:26:53: 5000000 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 19:26:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.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 19:26:56: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:26:56: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:26:58: 6000000 INFO @ Wed, 08 Dec 2021 19:27:01: 1000000 INFO @ Wed, 08 Dec 2021 19:27:04: 7000000 INFO @ Wed, 08 Dec 2021 19:27:07: 2000000 INFO @ Wed, 08 Dec 2021 19:27:10: 8000000 INFO @ Wed, 08 Dec 2021 19:27:12: 3000000 INFO @ Wed, 08 Dec 2021 19:27:15: 9000000 INFO @ Wed, 08 Dec 2021 19:27:18: 4000000 INFO @ Wed, 08 Dec 2021 19:27:21: 10000000 BedGraph に変換中... INFO @ Wed, 08 Dec 2021 19:27:24: 5000000 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 19:27:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.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 19:27:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:27:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:27:27: 11000000 INFO @ Wed, 08 Dec 2021 19:27:29: 6000000 INFO @ Wed, 08 Dec 2021 19:27:31: 1000000 INFO @ Wed, 08 Dec 2021 19:27:33: 12000000 INFO @ Wed, 08 Dec 2021 19:27:35: 7000000 INFO @ Wed, 08 Dec 2021 19:27:36: 2000000 INFO @ Wed, 08 Dec 2021 19:27:38: 13000000 INFO @ Wed, 08 Dec 2021 19:27:41: 8000000 INFO @ Wed, 08 Dec 2021 19:27:42: 3000000 INFO @ Wed, 08 Dec 2021 19:27:44: 14000000 INFO @ Wed, 08 Dec 2021 19:27:47: 4000000 INFO @ Wed, 08 Dec 2021 19:27:47: 9000000 INFO @ Wed, 08 Dec 2021 19:27:50: 15000000 INFO @ Wed, 08 Dec 2021 19:27:51: 5000000 INFO @ Wed, 08 Dec 2021 19:27:52: 10000000 INFO @ Wed, 08 Dec 2021 19:27:56: 16000000 INFO @ Wed, 08 Dec 2021 19:27:56: 6000000 INFO @ Wed, 08 Dec 2021 19:27:58: 11000000 INFO @ Wed, 08 Dec 2021 19:28:01: 7000000 INFO @ Wed, 08 Dec 2021 19:28:02: 17000000 INFO @ Wed, 08 Dec 2021 19:28:04: 12000000 INFO @ Wed, 08 Dec 2021 19:28:07: 8000000 INFO @ Wed, 08 Dec 2021 19:28:08: 18000000 INFO @ Wed, 08 Dec 2021 19:28:09: 13000000 INFO @ Wed, 08 Dec 2021 19:28:12: 9000000 INFO @ Wed, 08 Dec 2021 19:28:13: 19000000 INFO @ Wed, 08 Dec 2021 19:28:15: 14000000 INFO @ Wed, 08 Dec 2021 19:28:17: 10000000 INFO @ Wed, 08 Dec 2021 19:28:19: 20000000 INFO @ Wed, 08 Dec 2021 19:28:21: 15000000 INFO @ Wed, 08 Dec 2021 19:28:21: 11000000 INFO @ Wed, 08 Dec 2021 19:28:25: 21000000 INFO @ Wed, 08 Dec 2021 19:28:26: 12000000 INFO @ Wed, 08 Dec 2021 19:28:27: 16000000 INFO @ Wed, 08 Dec 2021 19:28:31: 22000000 INFO @ Wed, 08 Dec 2021 19:28:31: 13000000 INFO @ Wed, 08 Dec 2021 19:28:32: 17000000 INFO @ Wed, 08 Dec 2021 19:28:36: 14000000 INFO @ Wed, 08 Dec 2021 19:28:37: 23000000 INFO @ Wed, 08 Dec 2021 19:28:38: 18000000 INFO @ Wed, 08 Dec 2021 19:28:41: 15000000 INFO @ Wed, 08 Dec 2021 19:28:42: 24000000 INFO @ Wed, 08 Dec 2021 19:28:44: 19000000 INFO @ Wed, 08 Dec 2021 19:28:46: 16000000 INFO @ Wed, 08 Dec 2021 19:28:48: 25000000 INFO @ Wed, 08 Dec 2021 19:28:50: 20000000 INFO @ Wed, 08 Dec 2021 19:28:51: 17000000 INFO @ Wed, 08 Dec 2021 19:28:54: 26000000 INFO @ Wed, 08 Dec 2021 19:28:55: 21000000 INFO @ Wed, 08 Dec 2021 19:28:56: 18000000 INFO @ Wed, 08 Dec 2021 19:29:00: 27000000 INFO @ Wed, 08 Dec 2021 19:29:01: 22000000 INFO @ Wed, 08 Dec 2021 19:29:01: 19000000 INFO @ Wed, 08 Dec 2021 19:29:05: 28000000 INFO @ Wed, 08 Dec 2021 19:29:06: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:29:06: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:29:06: #1 total tags in treatment: 13115498 INFO @ Wed, 08 Dec 2021 19:29:06: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:29:06: #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 19:29:06: #1 tags after filtering in treatment: 12251895 INFO @ Wed, 08 Dec 2021 19:29:06: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:29:06: #1 finished! INFO @ Wed, 08 Dec 2021 19:29:06: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:29:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:29:06: 20000000 INFO @ Wed, 08 Dec 2021 19:29:07: 23000000 INFO @ Wed, 08 Dec 2021 19:29:07: #2 number of paired peaks: 349 WARNING @ Wed, 08 Dec 2021 19:29:07: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Wed, 08 Dec 2021 19:29:07: start model_add_line... INFO @ Wed, 08 Dec 2021 19:29:07: start X-correlation... INFO @ Wed, 08 Dec 2021 19:29:07: end of X-cor INFO @ Wed, 08 Dec 2021 19:29:07: #2 finished! INFO @ Wed, 08 Dec 2021 19:29:07: #2 predicted fragment length is 147 bps INFO @ Wed, 08 Dec 2021 19:29:07: #2 alternative fragment length(s) may be 4,147 bps INFO @ Wed, 08 Dec 2021 19:29:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.05_model.r INFO @ Wed, 08 Dec 2021 19:29:07: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:29:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:29:11: 21000000 INFO @ Wed, 08 Dec 2021 19:29:12: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:29:16: 22000000 INFO @ Wed, 08 Dec 2021 19:29:18: 25000000 INFO @ Wed, 08 Dec 2021 19:29:21: 23000000 INFO @ Wed, 08 Dec 2021 19:29:24: 26000000 INFO @ Wed, 08 Dec 2021 19:29:26: 24000000 INFO @ Wed, 08 Dec 2021 19:29:30: 27000000 INFO @ Wed, 08 Dec 2021 19:29:30: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:29:31: 25000000 INFO @ Wed, 08 Dec 2021 19:29:35: 28000000 INFO @ Wed, 08 Dec 2021 19:29:36: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:29:36: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:29:36: #1 total tags in treatment: 13115498 INFO @ Wed, 08 Dec 2021 19:29:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:29:36: #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 19:29:36: #1 tags after filtering in treatment: 12251895 INFO @ Wed, 08 Dec 2021 19:29:36: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:29:36: #1 finished! INFO @ Wed, 08 Dec 2021 19:29:36: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:29:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:29:36: 26000000 INFO @ Wed, 08 Dec 2021 19:29:37: #2 number of paired peaks: 349 WARNING @ Wed, 08 Dec 2021 19:29:37: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Wed, 08 Dec 2021 19:29:37: start model_add_line... INFO @ Wed, 08 Dec 2021 19:29:37: start X-correlation... INFO @ Wed, 08 Dec 2021 19:29:37: end of X-cor INFO @ Wed, 08 Dec 2021 19:29:37: #2 finished! INFO @ Wed, 08 Dec 2021 19:29:37: #2 predicted fragment length is 147 bps INFO @ Wed, 08 Dec 2021 19:29:37: #2 alternative fragment length(s) may be 4,147 bps INFO @ Wed, 08 Dec 2021 19:29:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.10_model.r INFO @ Wed, 08 Dec 2021 19:29:37: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:29:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:29:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:29:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:29:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.05_summits.bed INFO @ Wed, 08 Dec 2021 19:29:40: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (336 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:29:41: 27000000 INFO @ Wed, 08 Dec 2021 19:29:46: 28000000 INFO @ Wed, 08 Dec 2021 19:29:46: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:29:46: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:29:46: #1 total tags in treatment: 13115498 INFO @ Wed, 08 Dec 2021 19:29:46: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:29:46: #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 19:29:46: #1 tags after filtering in treatment: 12251895 INFO @ Wed, 08 Dec 2021 19:29:46: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:29:46: #1 finished! INFO @ Wed, 08 Dec 2021 19:29:46: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:29:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:29:47: #2 number of paired peaks: 349 WARNING @ Wed, 08 Dec 2021 19:29:47: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Wed, 08 Dec 2021 19:29:47: start model_add_line... INFO @ Wed, 08 Dec 2021 19:29:47: start X-correlation... INFO @ Wed, 08 Dec 2021 19:29:47: end of X-cor INFO @ Wed, 08 Dec 2021 19:29:47: #2 finished! INFO @ Wed, 08 Dec 2021 19:29:47: #2 predicted fragment length is 147 bps INFO @ Wed, 08 Dec 2021 19:29:47: #2 alternative fragment length(s) may be 4,147 bps INFO @ Wed, 08 Dec 2021 19:29:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.20_model.r INFO @ Wed, 08 Dec 2021 19:29:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:29:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:30:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:30:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:30:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:30:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:30:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.10_summits.bed INFO @ Wed, 08 Dec 2021 19:30:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:30:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:30:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:30:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976734/SRX8976734.20_summits.bed INFO @ Wed, 08 Dec 2021 19:30:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (185 records, 4 fields): 1 millis CompletedMACS2peakCalling