Job ID = 14157929 SRX = SRX10342601 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10014552 spots for SRR13964658/SRR13964658.sra Written 10014552 spots for SRR13964658/SRR13964658.sra Read 11034978 spots for SRR13964659/SRR13964659.sra Written 11034978 spots for SRR13964659/SRR13964659.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158183 ("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: 00:18:05 21049530 reads; of these: 21049530 (100.00%) were paired; of these: 5866512 (27.87%) aligned concordantly 0 times 13586986 (64.55%) aligned concordantly exactly 1 time 1596032 (7.58%) aligned concordantly >1 times ---- 5866512 pairs aligned concordantly 0 times; of these: 4314400 (73.54%) aligned discordantly 1 time ---- 1552112 pairs aligned 0 times concordantly or discordantly; of these: 3104224 mates make up the pairs; of these: 1542286 (49.68%) aligned 0 times 635709 (20.48%) aligned exactly 1 time 926229 (29.84%) aligned >1 times 96.34% overall alignment rate Time searching: 00:18:05 Overall time: 00:18:05 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] 3364752 / 19489837 = 0.1726 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 13:22:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.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 13:22:03: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:22:03: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:22:10: 1000000 INFO @ Wed, 08 Dec 2021 13:22:17: 2000000 INFO @ Wed, 08 Dec 2021 13:22:24: 3000000 INFO @ Wed, 08 Dec 2021 13:22:30: 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 13:22:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.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 13:22:33: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:22:33: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:22:36: 5000000 INFO @ Wed, 08 Dec 2021 13:22:40: 1000000 INFO @ Wed, 08 Dec 2021 13:22:43: 6000000 INFO @ Wed, 08 Dec 2021 13:22:46: 2000000 INFO @ Wed, 08 Dec 2021 13:22:49: 7000000 INFO @ Wed, 08 Dec 2021 13:22:53: 3000000 INFO @ Wed, 08 Dec 2021 13:22:55: 8000000 INFO @ Wed, 08 Dec 2021 13:23:00: 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 13:23:02: 9000000 INFO @ Wed, 08 Dec 2021 13:23:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.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 13:23:03: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:23:03: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:23:08: 5000000 INFO @ Wed, 08 Dec 2021 13:23:08: 10000000 INFO @ Wed, 08 Dec 2021 13:23:10: 1000000 INFO @ Wed, 08 Dec 2021 13:23:15: 6000000 INFO @ Wed, 08 Dec 2021 13:23:16: 11000000 INFO @ Wed, 08 Dec 2021 13:23:18: 2000000 INFO @ Wed, 08 Dec 2021 13:23:23: 7000000 INFO @ Wed, 08 Dec 2021 13:23:23: 12000000 INFO @ Wed, 08 Dec 2021 13:23:25: 3000000 INFO @ Wed, 08 Dec 2021 13:23:30: 13000000 INFO @ Wed, 08 Dec 2021 13:23:30: 8000000 INFO @ Wed, 08 Dec 2021 13:23:32: 4000000 INFO @ Wed, 08 Dec 2021 13:23:37: 14000000 INFO @ Wed, 08 Dec 2021 13:23:38: 9000000 INFO @ Wed, 08 Dec 2021 13:23:39: 5000000 INFO @ Wed, 08 Dec 2021 13:23:43: 15000000 INFO @ Wed, 08 Dec 2021 13:23:46: 10000000 INFO @ Wed, 08 Dec 2021 13:23:46: 6000000 INFO @ Wed, 08 Dec 2021 13:23:50: 16000000 INFO @ Wed, 08 Dec 2021 13:23:53: 7000000 INFO @ Wed, 08 Dec 2021 13:23:53: 11000000 INFO @ Wed, 08 Dec 2021 13:23:57: 17000000 INFO @ Wed, 08 Dec 2021 13:24:00: 8000000 INFO @ Wed, 08 Dec 2021 13:24:01: 12000000 INFO @ Wed, 08 Dec 2021 13:24:04: 18000000 INFO @ Wed, 08 Dec 2021 13:24:07: 9000000 INFO @ Wed, 08 Dec 2021 13:24:08: 13000000 INFO @ Wed, 08 Dec 2021 13:24:11: 19000000 INFO @ Wed, 08 Dec 2021 13:24:14: 10000000 INFO @ Wed, 08 Dec 2021 13:24:16: 14000000 INFO @ Wed, 08 Dec 2021 13:24:18: 20000000 INFO @ Wed, 08 Dec 2021 13:24:21: 11000000 INFO @ Wed, 08 Dec 2021 13:24:24: 15000000 INFO @ Wed, 08 Dec 2021 13:24:25: 21000000 INFO @ Wed, 08 Dec 2021 13:24:27: 12000000 INFO @ Wed, 08 Dec 2021 13:24:31: 22000000 INFO @ Wed, 08 Dec 2021 13:24:31: 16000000 INFO @ Wed, 08 Dec 2021 13:24:34: 13000000 INFO @ Wed, 08 Dec 2021 13:24:38: 23000000 INFO @ Wed, 08 Dec 2021 13:24:39: 17000000 INFO @ Wed, 08 Dec 2021 13:24:41: 14000000 INFO @ Wed, 08 Dec 2021 13:24:45: 24000000 INFO @ Wed, 08 Dec 2021 13:24:46: 18000000 INFO @ Wed, 08 Dec 2021 13:24:48: 15000000 INFO @ Wed, 08 Dec 2021 13:24:52: 25000000 INFO @ Wed, 08 Dec 2021 13:24:54: 19000000 INFO @ Wed, 08 Dec 2021 13:24:55: 16000000 INFO @ Wed, 08 Dec 2021 13:24:59: 26000000 INFO @ Wed, 08 Dec 2021 13:25:01: 20000000 INFO @ Wed, 08 Dec 2021 13:25:02: 17000000 INFO @ Wed, 08 Dec 2021 13:25:06: 27000000 INFO @ Wed, 08 Dec 2021 13:25:09: 21000000 INFO @ Wed, 08 Dec 2021 13:25:09: 18000000 INFO @ Wed, 08 Dec 2021 13:25:13: 28000000 INFO @ Wed, 08 Dec 2021 13:25:16: 22000000 INFO @ Wed, 08 Dec 2021 13:25:17: 19000000 INFO @ Wed, 08 Dec 2021 13:25:20: 29000000 INFO @ Wed, 08 Dec 2021 13:25:24: 20000000 INFO @ Wed, 08 Dec 2021 13:25:24: 23000000 INFO @ Wed, 08 Dec 2021 13:25:27: 30000000 INFO @ Wed, 08 Dec 2021 13:25:31: 21000000 INFO @ Wed, 08 Dec 2021 13:25:32: 24000000 INFO @ Wed, 08 Dec 2021 13:25:34: 31000000 INFO @ Wed, 08 Dec 2021 13:25:38: 22000000 INFO @ Wed, 08 Dec 2021 13:25:39: 25000000 INFO @ Wed, 08 Dec 2021 13:25:41: 32000000 INFO @ Wed, 08 Dec 2021 13:25:45: 23000000 INFO @ Wed, 08 Dec 2021 13:25:46: 26000000 INFO @ Wed, 08 Dec 2021 13:25:48: 33000000 INFO @ Wed, 08 Dec 2021 13:25:52: 24000000 INFO @ Wed, 08 Dec 2021 13:25:54: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 13:25:54: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 13:25:54: #1 total tags in treatment: 12377723 INFO @ Wed, 08 Dec 2021 13:25:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:25:54: #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 13:25:54: 27000000 INFO @ Wed, 08 Dec 2021 13:25:54: #1 tags after filtering in treatment: 11435075 INFO @ Wed, 08 Dec 2021 13:25:54: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 13:25:54: #1 finished! INFO @ Wed, 08 Dec 2021 13:25:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:25:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:25:55: #2 number of paired peaks: 515 WARNING @ Wed, 08 Dec 2021 13:25:55: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Wed, 08 Dec 2021 13:25:55: start model_add_line... INFO @ Wed, 08 Dec 2021 13:25:55: start X-correlation... INFO @ Wed, 08 Dec 2021 13:25:55: end of X-cor INFO @ Wed, 08 Dec 2021 13:25:55: #2 finished! INFO @ Wed, 08 Dec 2021 13:25:55: #2 predicted fragment length is 185 bps INFO @ Wed, 08 Dec 2021 13:25:55: #2 alternative fragment length(s) may be 4,185 bps INFO @ Wed, 08 Dec 2021 13:25:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.05_model.r INFO @ Wed, 08 Dec 2021 13:25:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:25:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 13:25:58: 25000000 INFO @ Wed, 08 Dec 2021 13:26:01: 28000000 INFO @ Wed, 08 Dec 2021 13:26:05: 26000000 INFO @ Wed, 08 Dec 2021 13:26:08: 29000000 INFO @ Wed, 08 Dec 2021 13:26:11: 27000000 INFO @ Wed, 08 Dec 2021 13:26:16: 30000000 INFO @ Wed, 08 Dec 2021 13:26:17: 28000000 INFO @ Wed, 08 Dec 2021 13:26:23: 31000000 INFO @ Wed, 08 Dec 2021 13:26:24: 29000000 INFO @ Wed, 08 Dec 2021 13:26:30: 30000000 INFO @ Wed, 08 Dec 2021 13:26:30: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:26:31: 32000000 INFO @ Wed, 08 Dec 2021 13:26:36: 31000000 INFO @ Wed, 08 Dec 2021 13:26:38: 33000000 INFO @ Wed, 08 Dec 2021 13:26:43: 32000000 INFO @ Wed, 08 Dec 2021 13:26:44: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 13:26:44: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 13:26:44: #1 total tags in treatment: 12377723 INFO @ Wed, 08 Dec 2021 13:26:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:26:44: #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 13:26:44: #1 tags after filtering in treatment: 11435075 INFO @ Wed, 08 Dec 2021 13:26:44: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 13:26:44: #1 finished! INFO @ Wed, 08 Dec 2021 13:26:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:26:45: #2 number of paired peaks: 515 WARNING @ Wed, 08 Dec 2021 13:26:45: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Wed, 08 Dec 2021 13:26:45: start model_add_line... INFO @ Wed, 08 Dec 2021 13:26:45: start X-correlation... INFO @ Wed, 08 Dec 2021 13:26:45: end of X-cor INFO @ Wed, 08 Dec 2021 13:26:45: #2 finished! INFO @ Wed, 08 Dec 2021 13:26:45: #2 predicted fragment length is 185 bps INFO @ Wed, 08 Dec 2021 13:26:45: #2 alternative fragment length(s) may be 4,185 bps INFO @ Wed, 08 Dec 2021 13:26:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.10_model.r INFO @ Wed, 08 Dec 2021 13:26:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:26:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:26:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.05_peaks.xls INFO @ Wed, 08 Dec 2021 13:26:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:26:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.05_summits.bed INFO @ Wed, 08 Dec 2021 13:26:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4982 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:26:49: 33000000 INFO @ Wed, 08 Dec 2021 13:26:54: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 13:26:54: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 13:26:54: #1 total tags in treatment: 12377723 INFO @ Wed, 08 Dec 2021 13:26:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:26:54: #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 13:26:54: #1 tags after filtering in treatment: 11435075 INFO @ Wed, 08 Dec 2021 13:26:54: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 13:26:54: #1 finished! INFO @ Wed, 08 Dec 2021 13:26:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:26:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:26:55: #2 number of paired peaks: 515 WARNING @ Wed, 08 Dec 2021 13:26:55: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Wed, 08 Dec 2021 13:26:55: start model_add_line... INFO @ Wed, 08 Dec 2021 13:26:55: start X-correlation... INFO @ Wed, 08 Dec 2021 13:26:55: end of X-cor INFO @ Wed, 08 Dec 2021 13:26:55: #2 finished! INFO @ Wed, 08 Dec 2021 13:26:55: #2 predicted fragment length is 185 bps INFO @ Wed, 08 Dec 2021 13:26:55: #2 alternative fragment length(s) may be 4,185 bps INFO @ Wed, 08 Dec 2021 13:26:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.20_model.r INFO @ Wed, 08 Dec 2021 13:26:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:26:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 13:27:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:27:30: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:27:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.10_peaks.xls INFO @ Wed, 08 Dec 2021 13:27:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:27:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.10_summits.bed INFO @ Wed, 08 Dec 2021 13:27:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3465 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:27:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.20_peaks.xls INFO @ Wed, 08 Dec 2021 13:27:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:27:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342601/SRX10342601.20_summits.bed INFO @ Wed, 08 Dec 2021 13:27:46: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1094 records, 4 fields): 5 millis CompletedMACS2peakCalling