Job ID = 6367719 SRX = SRX4029335 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:33:20 prefetch.2.10.7: 1) Downloading 'SRR7100995'... 2020-06-15T23:33:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:24 prefetch.2.10.7: 1) 'SRR7100995' was downloaded successfully 2020-06-15T23:45:24 prefetch.2.10.7: 'SRR7100995' has 0 unresolved dependencies Read 28701701 spots for SRR7100995/SRR7100995.sra Written 28701701 spots for SRR7100995/SRR7100995.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: 00:38:06 28701701 reads; of these: 28701701 (100.00%) were paired; of these: 3553003 (12.38%) aligned concordantly 0 times 22123177 (77.08%) aligned concordantly exactly 1 time 3025521 (10.54%) aligned concordantly >1 times ---- 3553003 pairs aligned concordantly 0 times; of these: 1697151 (47.77%) aligned discordantly 1 time ---- 1855852 pairs aligned 0 times concordantly or discordantly; of these: 3711704 mates make up the pairs; of these: 2385212 (64.26%) aligned 0 times 790275 (21.29%) aligned exactly 1 time 536217 (14.45%) aligned >1 times 95.84% overall alignment rate Time searching: 00:38:07 Overall time: 00:38:07 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 24 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] 6599136 / 26818531 = 0.2461 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 09:44:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.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 09:44:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:37: 1000000 INFO @ Tue, 16 Jun 2020 09:44:45: 2000000 INFO @ Tue, 16 Jun 2020 09:44:54: 3000000 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 09:44:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.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 09:44:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:03: 4000000 INFO @ Tue, 16 Jun 2020 09:45:09: 1000000 INFO @ Tue, 16 Jun 2020 09:45:12: 5000000 INFO @ Tue, 16 Jun 2020 09:45:18: 2000000 INFO @ Tue, 16 Jun 2020 09:45:22: 6000000 INFO @ Tue, 16 Jun 2020 09:45:27: 3000000 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 09:45:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.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 09:45:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:31: 7000000 INFO @ Tue, 16 Jun 2020 09:45:36: 4000000 INFO @ Tue, 16 Jun 2020 09:45:38: 1000000 INFO @ Tue, 16 Jun 2020 09:45:41: 8000000 INFO @ Tue, 16 Jun 2020 09:45:46: 5000000 INFO @ Tue, 16 Jun 2020 09:45:47: 2000000 INFO @ Tue, 16 Jun 2020 09:45:51: 9000000 INFO @ Tue, 16 Jun 2020 09:45:55: 6000000 INFO @ Tue, 16 Jun 2020 09:45:55: 3000000 INFO @ Tue, 16 Jun 2020 09:46:00: 10000000 INFO @ Tue, 16 Jun 2020 09:46:04: 4000000 INFO @ Tue, 16 Jun 2020 09:46:05: 7000000 INFO @ Tue, 16 Jun 2020 09:46:10: 11000000 INFO @ Tue, 16 Jun 2020 09:46:13: 5000000 INFO @ Tue, 16 Jun 2020 09:46:14: 8000000 INFO @ Tue, 16 Jun 2020 09:46:20: 12000000 INFO @ Tue, 16 Jun 2020 09:46:22: 6000000 INFO @ Tue, 16 Jun 2020 09:46:24: 9000000 INFO @ Tue, 16 Jun 2020 09:46:29: 13000000 INFO @ Tue, 16 Jun 2020 09:46:31: 7000000 INFO @ Tue, 16 Jun 2020 09:46:33: 10000000 INFO @ Tue, 16 Jun 2020 09:46:39: 14000000 INFO @ Tue, 16 Jun 2020 09:46:40: 8000000 INFO @ Tue, 16 Jun 2020 09:46:42: 11000000 INFO @ Tue, 16 Jun 2020 09:46:49: 15000000 INFO @ Tue, 16 Jun 2020 09:46:49: 9000000 INFO @ Tue, 16 Jun 2020 09:46:52: 12000000 INFO @ Tue, 16 Jun 2020 09:46:58: 10000000 INFO @ Tue, 16 Jun 2020 09:46:58: 16000000 INFO @ Tue, 16 Jun 2020 09:47:01: 13000000 INFO @ Tue, 16 Jun 2020 09:47:07: 11000000 INFO @ Tue, 16 Jun 2020 09:47:08: 17000000 INFO @ Tue, 16 Jun 2020 09:47:11: 14000000 INFO @ Tue, 16 Jun 2020 09:47:16: 12000000 INFO @ Tue, 16 Jun 2020 09:47:17: 18000000 INFO @ Tue, 16 Jun 2020 09:47:20: 15000000 INFO @ Tue, 16 Jun 2020 09:47:25: 13000000 INFO @ Tue, 16 Jun 2020 09:47:27: 19000000 INFO @ Tue, 16 Jun 2020 09:47:30: 16000000 INFO @ Tue, 16 Jun 2020 09:47:34: 14000000 INFO @ Tue, 16 Jun 2020 09:47:36: 20000000 INFO @ Tue, 16 Jun 2020 09:47:39: 17000000 INFO @ Tue, 16 Jun 2020 09:47:44: 15000000 INFO @ Tue, 16 Jun 2020 09:47:46: 21000000 INFO @ Tue, 16 Jun 2020 09:47:48: 18000000 INFO @ Tue, 16 Jun 2020 09:47:53: 16000000 INFO @ Tue, 16 Jun 2020 09:47:55: 22000000 INFO @ Tue, 16 Jun 2020 09:47:58: 19000000 INFO @ Tue, 16 Jun 2020 09:48:02: 17000000 INFO @ Tue, 16 Jun 2020 09:48:05: 23000000 INFO @ Tue, 16 Jun 2020 09:48:07: 20000000 INFO @ Tue, 16 Jun 2020 09:48:11: 18000000 INFO @ Tue, 16 Jun 2020 09:48:15: 24000000 INFO @ Tue, 16 Jun 2020 09:48:17: 21000000 INFO @ Tue, 16 Jun 2020 09:48:20: 19000000 INFO @ Tue, 16 Jun 2020 09:48:25: 25000000 INFO @ Tue, 16 Jun 2020 09:48:27: 22000000 INFO @ Tue, 16 Jun 2020 09:48:30: 20000000 INFO @ Tue, 16 Jun 2020 09:48:34: 26000000 INFO @ Tue, 16 Jun 2020 09:48:36: 23000000 INFO @ Tue, 16 Jun 2020 09:48:39: 21000000 INFO @ Tue, 16 Jun 2020 09:48:44: 27000000 INFO @ Tue, 16 Jun 2020 09:48:46: 24000000 INFO @ Tue, 16 Jun 2020 09:48:49: 22000000 INFO @ Tue, 16 Jun 2020 09:48:54: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:48:56: 25000000 INFO @ Tue, 16 Jun 2020 09:48:58: 23000000 INFO @ Tue, 16 Jun 2020 09:49:04: 29000000 INFO @ Tue, 16 Jun 2020 09:49:06: 26000000 INFO @ Tue, 16 Jun 2020 09:49:07: 24000000 INFO @ Tue, 16 Jun 2020 09:49:13: 30000000 INFO @ Tue, 16 Jun 2020 09:49:15: 27000000 INFO @ Tue, 16 Jun 2020 09:49:17: 25000000 INFO @ Tue, 16 Jun 2020 09:49:23: 31000000 INFO @ Tue, 16 Jun 2020 09:49:25: 28000000 INFO @ Tue, 16 Jun 2020 09:49:26: 26000000 INFO @ Tue, 16 Jun 2020 09:49:33: 32000000 INFO @ Tue, 16 Jun 2020 09:49:35: 29000000 INFO @ Tue, 16 Jun 2020 09:49:36: 27000000 INFO @ Tue, 16 Jun 2020 09:49:43: 33000000 INFO @ Tue, 16 Jun 2020 09:49:45: 30000000 INFO @ Tue, 16 Jun 2020 09:49:45: 28000000 INFO @ Tue, 16 Jun 2020 09:49:53: 34000000 INFO @ Tue, 16 Jun 2020 09:49:54: 29000000 INFO @ Tue, 16 Jun 2020 09:49:54: 31000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:50:03: 35000000 INFO @ Tue, 16 Jun 2020 09:50:04: 30000000 INFO @ Tue, 16 Jun 2020 09:50:04: 32000000 INFO @ Tue, 16 Jun 2020 09:50:13: 36000000 INFO @ Tue, 16 Jun 2020 09:50:13: 31000000 INFO @ Tue, 16 Jun 2020 09:50:14: 33000000 INFO @ Tue, 16 Jun 2020 09:50:22: 32000000 INFO @ Tue, 16 Jun 2020 09:50:23: 37000000 INFO @ Tue, 16 Jun 2020 09:50:24: 34000000 INFO @ Tue, 16 Jun 2020 09:50:32: 33000000 INFO @ Tue, 16 Jun 2020 09:50:33: 38000000 INFO @ Tue, 16 Jun 2020 09:50:34: 35000000 INFO @ Tue, 16 Jun 2020 09:50:41: 34000000 INFO @ Tue, 16 Jun 2020 09:50:43: 39000000 INFO @ Tue, 16 Jun 2020 09:50:44: 36000000 INFO @ Tue, 16 Jun 2020 09:50:50: 35000000 INFO @ Tue, 16 Jun 2020 09:50:53: 40000000 INFO @ Tue, 16 Jun 2020 09:50:54: 37000000 INFO @ Tue, 16 Jun 2020 09:51:00: 36000000 INFO @ Tue, 16 Jun 2020 09:51:03: 41000000 INFO @ Tue, 16 Jun 2020 09:51:04: 38000000 INFO @ Tue, 16 Jun 2020 09:51:09: 37000000 INFO @ Tue, 16 Jun 2020 09:51:11: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:51:11: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:51:11: #1 total tags in treatment: 18764331 INFO @ Tue, 16 Jun 2020 09:51:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:11: #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 09:51:11: #1 tags after filtering in treatment: 15885358 INFO @ Tue, 16 Jun 2020 09:51:11: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:51:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:12: #2 number of paired peaks: 633 WARNING @ Tue, 16 Jun 2020 09:51:12: Fewer paired peaks (633) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 633 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:13: #2 predicted fragment length is 225 bps INFO @ Tue, 16 Jun 2020 09:51:13: #2 alternative fragment length(s) may be 225 bps INFO @ Tue, 16 Jun 2020 09:51:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.05_model.r INFO @ Tue, 16 Jun 2020 09:51:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:14: 39000000 INFO @ Tue, 16 Jun 2020 09:51:18: 38000000 INFO @ Tue, 16 Jun 2020 09:51:23: 40000000 INFO @ Tue, 16 Jun 2020 09:51:27: 39000000 INFO @ Tue, 16 Jun 2020 09:51:33: 41000000 INFO @ Tue, 16 Jun 2020 09:51:36: 40000000 INFO @ Tue, 16 Jun 2020 09:51:41: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:51:41: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:51:41: #1 total tags in treatment: 18764331 INFO @ Tue, 16 Jun 2020 09:51:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:41: #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 09:51:41: #1 tags after filtering in treatment: 15885358 INFO @ Tue, 16 Jun 2020 09:51:41: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:51:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:43: #2 number of paired peaks: 633 WARNING @ Tue, 16 Jun 2020 09:51:43: Fewer paired peaks (633) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 633 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:43: #2 predicted fragment length is 225 bps INFO @ Tue, 16 Jun 2020 09:51:43: #2 alternative fragment length(s) may be 225 bps INFO @ Tue, 16 Jun 2020 09:51:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.10_model.r INFO @ Tue, 16 Jun 2020 09:51:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:44: 41000000 INFO @ Tue, 16 Jun 2020 09:51:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:50: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:51:50: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:51:50: #1 total tags in treatment: 18764331 INFO @ Tue, 16 Jun 2020 09:51:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:50: #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 09:51:50: #1 tags after filtering in treatment: 15885358 INFO @ Tue, 16 Jun 2020 09:51:50: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:51:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:51: #2 number of paired peaks: 633 WARNING @ Tue, 16 Jun 2020 09:51:51: Fewer paired peaks (633) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 633 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:52: #2 predicted fragment length is 225 bps INFO @ Tue, 16 Jun 2020 09:51:52: #2 alternative fragment length(s) may be 225 bps INFO @ Tue, 16 Jun 2020 09:51:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.20_model.r INFO @ Tue, 16 Jun 2020 09:51:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.05_summits.bed INFO @ Tue, 16 Jun 2020 09:52:08: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5552 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.10_summits.bed INFO @ Tue, 16 Jun 2020 09:52:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3823 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4029335/SRX4029335.20_summits.bed INFO @ Tue, 16 Jun 2020 09:52:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2180 records, 4 fields): 3 millis CompletedMACS2peakCalling