Job ID = 6367658 SRX = SRX3733152 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:35:05 prefetch.2.10.7: 1) Downloading 'SRR6760665'... 2020-06-15T23:35:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:29 prefetch.2.10.7: 1) 'SRR6760665' was downloaded successfully 2020-06-15T23:47:29 prefetch.2.10.7: 'SRR6760665' has 0 unresolved dependencies Read 35816431 spots for SRR6760665/SRR6760665.sra Written 35816431 spots for SRR6760665/SRR6760665.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:36:57 35816431 reads; of these: 35816431 (100.00%) were paired; of these: 3325577 (9.29%) aligned concordantly 0 times 30426432 (84.95%) aligned concordantly exactly 1 time 2064422 (5.76%) aligned concordantly >1 times ---- 3325577 pairs aligned concordantly 0 times; of these: 1423003 (42.79%) aligned discordantly 1 time ---- 1902574 pairs aligned 0 times concordantly or discordantly; of these: 3805148 mates make up the pairs; of these: 2735376 (71.89%) aligned 0 times 760598 (19.99%) aligned exactly 1 time 309174 (8.13%) aligned >1 times 96.18% overall alignment rate Time searching: 00:36:57 Overall time: 00:36:57 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 32 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] 13702682 / 33770428 = 0.4058 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:46:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.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 @ Tue, 16 Jun 2020 09:46:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:33: 1000000 INFO @ Tue, 16 Jun 2020 09:46:38: 2000000 INFO @ Tue, 16 Jun 2020 09:46:44: 3000000 INFO @ Tue, 16 Jun 2020 09:46:50: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:46:55: 5000000 INFO @ Tue, 16 Jun 2020 09:46:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.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 @ Tue, 16 Jun 2020 09:46:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:01: 6000000 INFO @ Tue, 16 Jun 2020 09:47:03: 1000000 INFO @ Tue, 16 Jun 2020 09:47:08: 7000000 INFO @ Tue, 16 Jun 2020 09:47:10: 2000000 INFO @ Tue, 16 Jun 2020 09:47:14: 8000000 INFO @ Tue, 16 Jun 2020 09:47:16: 3000000 INFO @ Tue, 16 Jun 2020 09:47:21: 9000000 INFO @ Tue, 16 Jun 2020 09:47:22: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:47:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.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 @ Tue, 16 Jun 2020 09:47:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:27: 10000000 INFO @ Tue, 16 Jun 2020 09:47:29: 5000000 INFO @ Tue, 16 Jun 2020 09:47:33: 1000000 INFO @ Tue, 16 Jun 2020 09:47:33: 11000000 INFO @ Tue, 16 Jun 2020 09:47:35: 6000000 INFO @ Tue, 16 Jun 2020 09:47:40: 2000000 INFO @ Tue, 16 Jun 2020 09:47:40: 12000000 INFO @ Tue, 16 Jun 2020 09:47:41: 7000000 INFO @ Tue, 16 Jun 2020 09:47:46: 3000000 INFO @ Tue, 16 Jun 2020 09:47:46: 13000000 INFO @ Tue, 16 Jun 2020 09:47:48: 8000000 INFO @ Tue, 16 Jun 2020 09:47:53: 4000000 INFO @ Tue, 16 Jun 2020 09:47:53: 14000000 INFO @ Tue, 16 Jun 2020 09:47:54: 9000000 INFO @ Tue, 16 Jun 2020 09:47:59: 5000000 INFO @ Tue, 16 Jun 2020 09:47:59: 15000000 INFO @ Tue, 16 Jun 2020 09:48:01: 10000000 INFO @ Tue, 16 Jun 2020 09:48:05: 6000000 INFO @ Tue, 16 Jun 2020 09:48:06: 16000000 INFO @ Tue, 16 Jun 2020 09:48:07: 11000000 INFO @ Tue, 16 Jun 2020 09:48:12: 17000000 INFO @ Tue, 16 Jun 2020 09:48:12: 7000000 INFO @ Tue, 16 Jun 2020 09:48:14: 12000000 INFO @ Tue, 16 Jun 2020 09:48:18: 18000000 INFO @ Tue, 16 Jun 2020 09:48:18: 8000000 INFO @ Tue, 16 Jun 2020 09:48:20: 13000000 INFO @ Tue, 16 Jun 2020 09:48:25: 19000000 INFO @ Tue, 16 Jun 2020 09:48:25: 9000000 INFO @ Tue, 16 Jun 2020 09:48:26: 14000000 INFO @ Tue, 16 Jun 2020 09:48:31: 20000000 INFO @ Tue, 16 Jun 2020 09:48:31: 10000000 INFO @ Tue, 16 Jun 2020 09:48:33: 15000000 INFO @ Tue, 16 Jun 2020 09:48:38: 21000000 INFO @ Tue, 16 Jun 2020 09:48:38: 11000000 INFO @ Tue, 16 Jun 2020 09:48:39: 16000000 INFO @ Tue, 16 Jun 2020 09:48:44: 22000000 INFO @ Tue, 16 Jun 2020 09:48:44: 12000000 INFO @ Tue, 16 Jun 2020 09:48:45: 17000000 INFO @ Tue, 16 Jun 2020 09:48:50: 23000000 INFO @ Tue, 16 Jun 2020 09:48:51: 13000000 INFO @ Tue, 16 Jun 2020 09:48:52: 18000000 INFO @ Tue, 16 Jun 2020 09:48:57: 24000000 INFO @ Tue, 16 Jun 2020 09:48:57: 14000000 INFO @ Tue, 16 Jun 2020 09:48:58: 19000000 INFO @ Tue, 16 Jun 2020 09:49:03: 25000000 INFO @ Tue, 16 Jun 2020 09:49:04: 15000000 INFO @ Tue, 16 Jun 2020 09:49:05: 20000000 INFO @ Tue, 16 Jun 2020 09:49:10: 26000000 INFO @ Tue, 16 Jun 2020 09:49:10: 16000000 INFO @ Tue, 16 Jun 2020 09:49:11: 21000000 INFO @ Tue, 16 Jun 2020 09:49:16: 27000000 INFO @ Tue, 16 Jun 2020 09:49:16: 17000000 INFO @ Tue, 16 Jun 2020 09:49:18: 22000000 INFO @ Tue, 16 Jun 2020 09:49:23: 28000000 INFO @ Tue, 16 Jun 2020 09:49:23: 18000000 INFO @ Tue, 16 Jun 2020 09:49:24: 23000000 INFO @ Tue, 16 Jun 2020 09:49:29: 29000000 INFO @ Tue, 16 Jun 2020 09:49:30: 19000000 INFO @ Tue, 16 Jun 2020 09:49:31: 24000000 INFO @ Tue, 16 Jun 2020 09:49:36: 30000000 INFO @ Tue, 16 Jun 2020 09:49:36: 20000000 INFO @ Tue, 16 Jun 2020 09:49:37: 25000000 INFO @ Tue, 16 Jun 2020 09:49:42: 21000000 INFO @ Tue, 16 Jun 2020 09:49:43: 31000000 INFO @ Tue, 16 Jun 2020 09:49:43: 26000000 INFO @ Tue, 16 Jun 2020 09:49:49: 22000000 INFO @ Tue, 16 Jun 2020 09:49:49: 32000000 INFO @ Tue, 16 Jun 2020 09:49:50: 27000000 INFO @ Tue, 16 Jun 2020 09:49:56: 23000000 INFO @ Tue, 16 Jun 2020 09:49:56: 33000000 INFO @ Tue, 16 Jun 2020 09:49:56: 28000000 INFO @ Tue, 16 Jun 2020 09:50:02: 34000000 INFO @ Tue, 16 Jun 2020 09:50:02: 24000000 INFO @ Tue, 16 Jun 2020 09:50:03: 29000000 INFO @ Tue, 16 Jun 2020 09:50:08: 35000000 INFO @ Tue, 16 Jun 2020 09:50:09: 25000000 INFO @ Tue, 16 Jun 2020 09:50:09: 30000000 INFO @ Tue, 16 Jun 2020 09:50:15: 36000000 INFO @ Tue, 16 Jun 2020 09:50:15: 26000000 INFO @ Tue, 16 Jun 2020 09:50:16: 31000000 INFO @ Tue, 16 Jun 2020 09:50:22: 37000000 INFO @ Tue, 16 Jun 2020 09:50:22: 27000000 INFO @ Tue, 16 Jun 2020 09:50:22: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:50:28: 38000000 INFO @ Tue, 16 Jun 2020 09:50:28: 28000000 INFO @ Tue, 16 Jun 2020 09:50:29: 33000000 INFO @ Tue, 16 Jun 2020 09:50:35: 39000000 INFO @ Tue, 16 Jun 2020 09:50:35: 29000000 INFO @ Tue, 16 Jun 2020 09:50:35: 34000000 INFO @ Tue, 16 Jun 2020 09:50:41: 40000000 INFO @ Tue, 16 Jun 2020 09:50:41: 30000000 INFO @ Tue, 16 Jun 2020 09:50:42: 35000000 INFO @ Tue, 16 Jun 2020 09:50:48: 41000000 INFO @ Tue, 16 Jun 2020 09:50:48: 31000000 INFO @ Tue, 16 Jun 2020 09:50:48: 36000000 INFO @ Tue, 16 Jun 2020 09:50:51: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:50:51: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:50:51: #1 total tags in treatment: 19144625 INFO @ Tue, 16 Jun 2020 09:50:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:50:51: #1 tags after filtering in treatment: 15929939 INFO @ Tue, 16 Jun 2020 09:50:51: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 16 Jun 2020 09:50:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:53: #2 number of paired peaks: 813 WARNING @ Tue, 16 Jun 2020 09:50:53: Fewer paired peaks (813) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 813 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:53: #2 predicted fragment length is 213 bps INFO @ Tue, 16 Jun 2020 09:50:53: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 16 Jun 2020 09:50:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.05_model.r INFO @ Tue, 16 Jun 2020 09:50:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:54: 32000000 INFO @ Tue, 16 Jun 2020 09:50:55: 37000000 INFO @ Tue, 16 Jun 2020 09:51:01: 33000000 INFO @ Tue, 16 Jun 2020 09:51:01: 38000000 INFO @ Tue, 16 Jun 2020 09:51:07: 34000000 INFO @ Tue, 16 Jun 2020 09:51:07: 39000000 INFO @ Tue, 16 Jun 2020 09:51:14: 35000000 INFO @ Tue, 16 Jun 2020 09:51:14: 40000000 INFO @ Tue, 16 Jun 2020 09:51:20: 36000000 INFO @ Tue, 16 Jun 2020 09:51:20: 41000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:51:24: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:51:24: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:51:24: #1 total tags in treatment: 19144625 INFO @ Tue, 16 Jun 2020 09:51:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:51:24: #1 tags after filtering in treatment: 15929939 INFO @ Tue, 16 Jun 2020 09:51:24: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 16 Jun 2020 09:51:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:25: #2 number of paired peaks: 813 WARNING @ Tue, 16 Jun 2020 09:51:25: Fewer paired peaks (813) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 813 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:25: #2 predicted fragment length is 213 bps INFO @ Tue, 16 Jun 2020 09:51:25: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 16 Jun 2020 09:51:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.10_model.r INFO @ Tue, 16 Jun 2020 09:51:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:26: 37000000 INFO @ Tue, 16 Jun 2020 09:51:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:33: 38000000 INFO @ Tue, 16 Jun 2020 09:51:39: 39000000 INFO @ Tue, 16 Jun 2020 09:51:45: 40000000 INFO @ Tue, 16 Jun 2020 09:51:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.05_summits.bed INFO @ Tue, 16 Jun 2020 09:51:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4763 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:51: 41000000 INFO @ Tue, 16 Jun 2020 09:51:54: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:51:54: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:51:54: #1 total tags in treatment: 19144625 INFO @ Tue, 16 Jun 2020 09:51:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:51:54: #1 tags after filtering in treatment: 15929939 INFO @ Tue, 16 Jun 2020 09:51:54: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 16 Jun 2020 09:51:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:55: #2 number of paired peaks: 813 WARNING @ Tue, 16 Jun 2020 09:51:55: Fewer paired peaks (813) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 813 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:55: #2 predicted fragment length is 213 bps INFO @ Tue, 16 Jun 2020 09:51:55: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 16 Jun 2020 09:51:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.20_model.r INFO @ Tue, 16 Jun 2020 09:51:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.10_summits.bed INFO @ Tue, 16 Jun 2020 09:52:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2857 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733152/SRX3733152.20_summits.bed INFO @ Tue, 16 Jun 2020 09:52:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1407 records, 4 fields): 2 millis CompletedMACS2peakCalling