Job ID = 14159432 SRX = SRX8976692 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17389682 spots for SRR12483296/SRR12483296.sra Written 17389682 spots for SRR12483296/SRR12483296.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159635 ("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: 00:14:35 17389682 reads; of these: 17389682 (100.00%) were paired; of these: 1959079 (11.27%) aligned concordantly 0 times 12432879 (71.50%) aligned concordantly exactly 1 time 2997724 (17.24%) aligned concordantly >1 times ---- 1959079 pairs aligned concordantly 0 times; of these: 1206259 (61.57%) aligned discordantly 1 time ---- 752820 pairs aligned 0 times concordantly or discordantly; of these: 1505640 mates make up the pairs; of these: 534950 (35.53%) aligned 0 times 359752 (23.89%) aligned exactly 1 time 610938 (40.58%) aligned >1 times 98.46% overall alignment rate Time searching: 00:14:35 Overall time: 00:14:35 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] 1495478 / 16624518 = 0.0900 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 22:06:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.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 22:06:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:06:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:06:15: 1000000 INFO @ Wed, 08 Dec 2021 22:06:21: 2000000 INFO @ Wed, 08 Dec 2021 22:06:27: 3000000 INFO @ Wed, 08 Dec 2021 22:06:34: 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 22:06:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.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 22:06:39: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:06:39: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:06:40: 5000000 INFO @ Wed, 08 Dec 2021 22:06:46: 1000000 INFO @ Wed, 08 Dec 2021 22:06:47: 6000000 INFO @ Wed, 08 Dec 2021 22:06:52: 2000000 INFO @ Wed, 08 Dec 2021 22:06:54: 7000000 INFO @ Wed, 08 Dec 2021 22:06:59: 3000000 INFO @ Wed, 08 Dec 2021 22:07:00: 8000000 INFO @ Wed, 08 Dec 2021 22:07:06: 4000000 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 22:07:07: 9000000 INFO @ Wed, 08 Dec 2021 22:07:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.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 22:07:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:07:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:07:13: 5000000 INFO @ Wed, 08 Dec 2021 22:07:14: 10000000 INFO @ Wed, 08 Dec 2021 22:07:15: 1000000 INFO @ Wed, 08 Dec 2021 22:07:20: 6000000 INFO @ Wed, 08 Dec 2021 22:07:21: 11000000 INFO @ Wed, 08 Dec 2021 22:07:22: 2000000 INFO @ Wed, 08 Dec 2021 22:07:27: 7000000 INFO @ Wed, 08 Dec 2021 22:07:28: 12000000 INFO @ Wed, 08 Dec 2021 22:07:28: 3000000 INFO @ Wed, 08 Dec 2021 22:07:34: 8000000 INFO @ Wed, 08 Dec 2021 22:07:35: 13000000 INFO @ Wed, 08 Dec 2021 22:07:35: 4000000 INFO @ Wed, 08 Dec 2021 22:07:41: 5000000 INFO @ Wed, 08 Dec 2021 22:07:41: 9000000 INFO @ Wed, 08 Dec 2021 22:07:42: 14000000 INFO @ Wed, 08 Dec 2021 22:07:48: 6000000 INFO @ Wed, 08 Dec 2021 22:07:48: 10000000 INFO @ Wed, 08 Dec 2021 22:07:48: 15000000 INFO @ Wed, 08 Dec 2021 22:07:54: 7000000 INFO @ Wed, 08 Dec 2021 22:07:55: 11000000 INFO @ Wed, 08 Dec 2021 22:07:55: 16000000 INFO @ Wed, 08 Dec 2021 22:08:00: 8000000 INFO @ Wed, 08 Dec 2021 22:08:02: 17000000 INFO @ Wed, 08 Dec 2021 22:08:02: 12000000 INFO @ Wed, 08 Dec 2021 22:08:07: 9000000 INFO @ Wed, 08 Dec 2021 22:08:09: 18000000 INFO @ Wed, 08 Dec 2021 22:08:09: 13000000 INFO @ Wed, 08 Dec 2021 22:08:13: 10000000 INFO @ Wed, 08 Dec 2021 22:08:16: 19000000 INFO @ Wed, 08 Dec 2021 22:08:16: 14000000 INFO @ Wed, 08 Dec 2021 22:08:20: 11000000 INFO @ Wed, 08 Dec 2021 22:08:23: 15000000 INFO @ Wed, 08 Dec 2021 22:08:23: 20000000 INFO @ Wed, 08 Dec 2021 22:08:26: 12000000 INFO @ Wed, 08 Dec 2021 22:08:30: 16000000 INFO @ Wed, 08 Dec 2021 22:08:30: 21000000 INFO @ Wed, 08 Dec 2021 22:08:32: 13000000 INFO @ Wed, 08 Dec 2021 22:08:37: 17000000 INFO @ Wed, 08 Dec 2021 22:08:37: 22000000 INFO @ Wed, 08 Dec 2021 22:08:39: 14000000 INFO @ Wed, 08 Dec 2021 22:08:43: 18000000 INFO @ Wed, 08 Dec 2021 22:08:44: 23000000 INFO @ Wed, 08 Dec 2021 22:08:45: 15000000 INFO @ Wed, 08 Dec 2021 22:08:50: 19000000 INFO @ Wed, 08 Dec 2021 22:08:51: 24000000 INFO @ Wed, 08 Dec 2021 22:08:51: 16000000 INFO @ Wed, 08 Dec 2021 22:08:57: 20000000 INFO @ Wed, 08 Dec 2021 22:08:57: 25000000 INFO @ Wed, 08 Dec 2021 22:08:58: 17000000 INFO @ Wed, 08 Dec 2021 22:09:04: 21000000 INFO @ Wed, 08 Dec 2021 22:09:04: 18000000 INFO @ Wed, 08 Dec 2021 22:09:04: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:09:10: 19000000 INFO @ Wed, 08 Dec 2021 22:09:10: 22000000 INFO @ Wed, 08 Dec 2021 22:09:11: 27000000 INFO @ Wed, 08 Dec 2021 22:09:17: 20000000 INFO @ Wed, 08 Dec 2021 22:09:17: 23000000 INFO @ Wed, 08 Dec 2021 22:09:18: 28000000 INFO @ Wed, 08 Dec 2021 22:09:23: 21000000 INFO @ Wed, 08 Dec 2021 22:09:24: 24000000 INFO @ Wed, 08 Dec 2021 22:09:25: 29000000 INFO @ Wed, 08 Dec 2021 22:09:30: 22000000 INFO @ Wed, 08 Dec 2021 22:09:31: 25000000 INFO @ Wed, 08 Dec 2021 22:09:32: 30000000 INFO @ Wed, 08 Dec 2021 22:09:36: 23000000 INFO @ Wed, 08 Dec 2021 22:09:37: 26000000 INFO @ Wed, 08 Dec 2021 22:09:39: 31000000 INFO @ Wed, 08 Dec 2021 22:09:41: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:09:41: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:09:41: #1 total tags in treatment: 14012661 INFO @ Wed, 08 Dec 2021 22:09:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:09:41: #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 22:09:41: #1 tags after filtering in treatment: 12311017 INFO @ Wed, 08 Dec 2021 22:09:41: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 08 Dec 2021 22:09:41: #1 finished! INFO @ Wed, 08 Dec 2021 22:09:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:09:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:09:42: #2 number of paired peaks: 592 WARNING @ Wed, 08 Dec 2021 22:09:42: Fewer paired peaks (592) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 592 pairs to build model! INFO @ Wed, 08 Dec 2021 22:09:42: start model_add_line... INFO @ Wed, 08 Dec 2021 22:09:42: start X-correlation... INFO @ Wed, 08 Dec 2021 22:09:42: end of X-cor INFO @ Wed, 08 Dec 2021 22:09:42: #2 finished! INFO @ Wed, 08 Dec 2021 22:09:42: #2 predicted fragment length is 132 bps INFO @ Wed, 08 Dec 2021 22:09:42: #2 alternative fragment length(s) may be 3,132,145 bps INFO @ Wed, 08 Dec 2021 22:09:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.05_model.r INFO @ Wed, 08 Dec 2021 22:09:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:09:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:09:43: 24000000 INFO @ Wed, 08 Dec 2021 22:09:44: 27000000 INFO @ Wed, 08 Dec 2021 22:09:49: 25000000 INFO @ Wed, 08 Dec 2021 22:09:51: 28000000 INFO @ Wed, 08 Dec 2021 22:09:55: 26000000 INFO @ Wed, 08 Dec 2021 22:09:57: 29000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:10:01: 27000000 INFO @ Wed, 08 Dec 2021 22:10:04: 30000000 INFO @ Wed, 08 Dec 2021 22:10:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:10:07: 28000000 INFO @ Wed, 08 Dec 2021 22:10:11: 31000000 INFO @ Wed, 08 Dec 2021 22:10:12: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:10:12: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:10:12: #1 total tags in treatment: 14012661 INFO @ Wed, 08 Dec 2021 22:10:12: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:10:12: #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 22:10:12: #1 tags after filtering in treatment: 12311017 INFO @ Wed, 08 Dec 2021 22:10:12: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 08 Dec 2021 22:10:12: #1 finished! INFO @ Wed, 08 Dec 2021 22:10:12: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:10:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:10:13: 29000000 INFO @ Wed, 08 Dec 2021 22:10:13: #2 number of paired peaks: 592 WARNING @ Wed, 08 Dec 2021 22:10:13: Fewer paired peaks (592) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 592 pairs to build model! INFO @ Wed, 08 Dec 2021 22:10:13: start model_add_line... INFO @ Wed, 08 Dec 2021 22:10:13: start X-correlation... INFO @ Wed, 08 Dec 2021 22:10:13: end of X-cor INFO @ Wed, 08 Dec 2021 22:10:13: #2 finished! INFO @ Wed, 08 Dec 2021 22:10:13: #2 predicted fragment length is 132 bps INFO @ Wed, 08 Dec 2021 22:10:13: #2 alternative fragment length(s) may be 3,132,145 bps INFO @ Wed, 08 Dec 2021 22:10:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.10_model.r INFO @ Wed, 08 Dec 2021 22:10:13: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:10:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:10:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:10:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:10:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.05_summits.bed INFO @ Wed, 08 Dec 2021 22:10:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (561 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:10:18: 30000000 INFO @ Wed, 08 Dec 2021 22:10:24: 31000000 INFO @ Wed, 08 Dec 2021 22:10:25: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:10:25: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:10:25: #1 total tags in treatment: 14012661 INFO @ Wed, 08 Dec 2021 22:10:25: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:10:25: #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 22:10:25: #1 tags after filtering in treatment: 12311017 INFO @ Wed, 08 Dec 2021 22:10:25: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 08 Dec 2021 22:10:25: #1 finished! INFO @ Wed, 08 Dec 2021 22:10:25: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:10:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:10:26: #2 number of paired peaks: 592 WARNING @ Wed, 08 Dec 2021 22:10:26: Fewer paired peaks (592) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 592 pairs to build model! INFO @ Wed, 08 Dec 2021 22:10:26: start model_add_line... INFO @ Wed, 08 Dec 2021 22:10:26: start X-correlation... INFO @ Wed, 08 Dec 2021 22:10:26: end of X-cor INFO @ Wed, 08 Dec 2021 22:10:26: #2 finished! INFO @ Wed, 08 Dec 2021 22:10:26: #2 predicted fragment length is 132 bps INFO @ Wed, 08 Dec 2021 22:10:26: #2 alternative fragment length(s) may be 3,132,145 bps INFO @ Wed, 08 Dec 2021 22:10:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.20_model.r INFO @ Wed, 08 Dec 2021 22:10:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:10:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:10:38: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:10:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:10:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:10:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.10_summits.bed INFO @ Wed, 08 Dec 2021 22:10:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (318 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:10:52: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:11:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:11:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:11:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976692/SRX8976692.20_summits.bed INFO @ Wed, 08 Dec 2021 22:11:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (206 records, 4 fields): 1 millis CompletedMACS2peakCalling