Job ID = 6367663 SRX = SRX3733157 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:32:50 prefetch.2.10.7: 1) Downloading 'SRR6760670'... 2020-06-15T23:32:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:19 prefetch.2.10.7: 1) 'SRR6760670' was downloaded successfully 2020-06-15T23:48:19 prefetch.2.10.7: 'SRR6760670' has 0 unresolved dependencies Read 37064952 spots for SRR6760670/SRR6760670.sra Written 37064952 spots for SRR6760670/SRR6760670.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: 00:40:57 37064952 reads; of these: 37064952 (100.00%) were paired; of these: 2372984 (6.40%) aligned concordantly 0 times 32420997 (87.47%) aligned concordantly exactly 1 time 2270971 (6.13%) aligned concordantly >1 times ---- 2372984 pairs aligned concordantly 0 times; of these: 579069 (24.40%) aligned discordantly 1 time ---- 1793915 pairs aligned 0 times concordantly or discordantly; of these: 3587830 mates make up the pairs; of these: 2817060 (78.52%) aligned 0 times 573182 (15.98%) aligned exactly 1 time 197588 (5.51%) aligned >1 times 96.20% overall alignment rate Time searching: 00:40:57 Overall time: 00:40:57 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] 14082445 / 35121770 = 0.4010 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 09:55:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.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 09:55:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:46: 1000000 INFO @ Tue, 16 Jun 2020 09:55:51: 2000000 INFO @ Tue, 16 Jun 2020 09:55:57: 3000000 INFO @ Tue, 16 Jun 2020 09:56:03: 4000000 INFO @ Tue, 16 Jun 2020 09:56:09: 5000000 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 09:56:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.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 09:56:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:56:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:56:15: 6000000 INFO @ Tue, 16 Jun 2020 09:56:17: 1000000 INFO @ Tue, 16 Jun 2020 09:56:22: 7000000 INFO @ Tue, 16 Jun 2020 09:56:23: 2000000 INFO @ Tue, 16 Jun 2020 09:56:28: 8000000 INFO @ Tue, 16 Jun 2020 09:56:30: 3000000 INFO @ Tue, 16 Jun 2020 09:56:33: 9000000 INFO @ Tue, 16 Jun 2020 09:56:36: 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 09:56:39: 10000000 INFO @ Tue, 16 Jun 2020 09:56:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.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 09:56:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:56:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:56:42: 5000000 INFO @ Tue, 16 Jun 2020 09:56:45: 11000000 INFO @ Tue, 16 Jun 2020 09:56:47: 1000000 INFO @ Tue, 16 Jun 2020 09:56:48: 6000000 INFO @ Tue, 16 Jun 2020 09:56:51: 12000000 INFO @ Tue, 16 Jun 2020 09:56:53: 2000000 INFO @ Tue, 16 Jun 2020 09:56:54: 7000000 INFO @ Tue, 16 Jun 2020 09:56:57: 13000000 INFO @ Tue, 16 Jun 2020 09:56:59: 3000000 INFO @ Tue, 16 Jun 2020 09:57:00: 8000000 INFO @ Tue, 16 Jun 2020 09:57:04: 14000000 INFO @ Tue, 16 Jun 2020 09:57:05: 4000000 INFO @ Tue, 16 Jun 2020 09:57:07: 9000000 INFO @ Tue, 16 Jun 2020 09:57:10: 15000000 INFO @ Tue, 16 Jun 2020 09:57:11: 5000000 INFO @ Tue, 16 Jun 2020 09:57:13: 10000000 INFO @ Tue, 16 Jun 2020 09:57:16: 16000000 INFO @ Tue, 16 Jun 2020 09:57:18: 6000000 INFO @ Tue, 16 Jun 2020 09:57:20: 11000000 INFO @ Tue, 16 Jun 2020 09:57:22: 17000000 INFO @ Tue, 16 Jun 2020 09:57:24: 7000000 INFO @ Tue, 16 Jun 2020 09:57:26: 12000000 INFO @ Tue, 16 Jun 2020 09:57:28: 18000000 INFO @ Tue, 16 Jun 2020 09:57:30: 8000000 INFO @ Tue, 16 Jun 2020 09:57:33: 13000000 INFO @ Tue, 16 Jun 2020 09:57:34: 19000000 INFO @ Tue, 16 Jun 2020 09:57:36: 9000000 INFO @ Tue, 16 Jun 2020 09:57:39: 14000000 INFO @ Tue, 16 Jun 2020 09:57:40: 20000000 INFO @ Tue, 16 Jun 2020 09:57:42: 10000000 INFO @ Tue, 16 Jun 2020 09:57:46: 21000000 INFO @ Tue, 16 Jun 2020 09:57:46: 15000000 INFO @ Tue, 16 Jun 2020 09:57:48: 11000000 INFO @ Tue, 16 Jun 2020 09:57:52: 22000000 INFO @ Tue, 16 Jun 2020 09:57:53: 16000000 INFO @ Tue, 16 Jun 2020 09:57:54: 12000000 INFO @ Tue, 16 Jun 2020 09:57:58: 23000000 INFO @ Tue, 16 Jun 2020 09:57:59: 17000000 INFO @ Tue, 16 Jun 2020 09:58:00: 13000000 INFO @ Tue, 16 Jun 2020 09:58:04: 24000000 INFO @ Tue, 16 Jun 2020 09:58:06: 18000000 INFO @ Tue, 16 Jun 2020 09:58:06: 14000000 INFO @ Tue, 16 Jun 2020 09:58:10: 25000000 INFO @ Tue, 16 Jun 2020 09:58:12: 19000000 INFO @ Tue, 16 Jun 2020 09:58:12: 15000000 INFO @ Tue, 16 Jun 2020 09:58:16: 26000000 INFO @ Tue, 16 Jun 2020 09:58:18: 16000000 INFO @ Tue, 16 Jun 2020 09:58:18: 20000000 INFO @ Tue, 16 Jun 2020 09:58:22: 27000000 INFO @ Tue, 16 Jun 2020 09:58:24: 17000000 INFO @ Tue, 16 Jun 2020 09:58:25: 21000000 INFO @ Tue, 16 Jun 2020 09:58:28: 28000000 INFO @ Tue, 16 Jun 2020 09:58:31: 18000000 INFO @ Tue, 16 Jun 2020 09:58:32: 22000000 INFO @ Tue, 16 Jun 2020 09:58:34: 29000000 INFO @ Tue, 16 Jun 2020 09:58:37: 19000000 INFO @ Tue, 16 Jun 2020 09:58:38: 23000000 INFO @ Tue, 16 Jun 2020 09:58:40: 30000000 INFO @ Tue, 16 Jun 2020 09:58:43: 20000000 INFO @ Tue, 16 Jun 2020 09:58:45: 24000000 INFO @ Tue, 16 Jun 2020 09:58:47: 31000000 INFO @ Tue, 16 Jun 2020 09:58:49: 21000000 INFO @ Tue, 16 Jun 2020 09:58:52: 25000000 INFO @ Tue, 16 Jun 2020 09:58:53: 32000000 INFO @ Tue, 16 Jun 2020 09:58:55: 22000000 INFO @ Tue, 16 Jun 2020 09:58:58: 26000000 INFO @ Tue, 16 Jun 2020 09:59:00: 33000000 INFO @ Tue, 16 Jun 2020 09:59:02: 23000000 INFO @ Tue, 16 Jun 2020 09:59:05: 27000000 INFO @ Tue, 16 Jun 2020 09:59:06: 34000000 INFO @ Tue, 16 Jun 2020 09:59:08: 24000000 INFO @ Tue, 16 Jun 2020 09:59:12: 28000000 INFO @ Tue, 16 Jun 2020 09:59:12: 35000000 INFO @ Tue, 16 Jun 2020 09:59:14: 25000000 INFO @ Tue, 16 Jun 2020 09:59:18: 36000000 INFO @ Tue, 16 Jun 2020 09:59:18: 29000000 INFO @ Tue, 16 Jun 2020 09:59:20: 26000000 INFO @ Tue, 16 Jun 2020 09:59:24: 37000000 INFO @ Tue, 16 Jun 2020 09:59:25: 30000000 INFO @ Tue, 16 Jun 2020 09:59:27: 27000000 INFO @ Tue, 16 Jun 2020 09:59:30: 38000000 INFO @ Tue, 16 Jun 2020 09:59:32: 31000000 INFO @ Tue, 16 Jun 2020 09:59:33: 28000000 INFO @ Tue, 16 Jun 2020 09:59:37: 39000000 INFO @ Tue, 16 Jun 2020 09:59:38: 32000000 INFO @ Tue, 16 Jun 2020 09:59:39: 29000000 INFO @ Tue, 16 Jun 2020 09:59:43: 40000000 INFO @ Tue, 16 Jun 2020 09:59:45: 33000000 INFO @ Tue, 16 Jun 2020 09:59:46: 30000000 INFO @ Tue, 16 Jun 2020 09:59:49: 41000000 INFO @ Tue, 16 Jun 2020 09:59:52: 34000000 INFO @ Tue, 16 Jun 2020 09:59:52: 31000000 INFO @ Tue, 16 Jun 2020 09:59:56: 42000000 INFO @ Tue, 16 Jun 2020 09:59:58: 35000000 INFO @ Tue, 16 Jun 2020 09:59:58: 32000000 INFO @ Tue, 16 Jun 2020 10:00:02: 43000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:00:03: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:00:03: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:00:03: #1 total tags in treatment: 20679171 INFO @ Tue, 16 Jun 2020 10:00:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:00:03: #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 10:00:03: #1 tags after filtering in treatment: 17174443 INFO @ Tue, 16 Jun 2020 10:00:03: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 16 Jun 2020 10:00:03: #1 finished! INFO @ Tue, 16 Jun 2020 10:00:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:00:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:00:05: 33000000 INFO @ Tue, 16 Jun 2020 10:00:05: #2 number of paired peaks: 681 WARNING @ Tue, 16 Jun 2020 10:00:05: Fewer paired peaks (681) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 681 pairs to build model! INFO @ Tue, 16 Jun 2020 10:00:05: start model_add_line... INFO @ Tue, 16 Jun 2020 10:00:05: start X-correlation... INFO @ Tue, 16 Jun 2020 10:00:05: end of X-cor INFO @ Tue, 16 Jun 2020 10:00:05: #2 finished! INFO @ Tue, 16 Jun 2020 10:00:05: #2 predicted fragment length is 198 bps INFO @ Tue, 16 Jun 2020 10:00:05: #2 alternative fragment length(s) may be 4,198 bps INFO @ Tue, 16 Jun 2020 10:00:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.05_model.r INFO @ Tue, 16 Jun 2020 10:00:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:00:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:00:05: 36000000 INFO @ Tue, 16 Jun 2020 10:00:11: 34000000 INFO @ Tue, 16 Jun 2020 10:00:12: 37000000 INFO @ Tue, 16 Jun 2020 10:00:17: 35000000 INFO @ Tue, 16 Jun 2020 10:00:18: 38000000 INFO @ Tue, 16 Jun 2020 10:00:23: 36000000 INFO @ Tue, 16 Jun 2020 10:00:25: 39000000 INFO @ Tue, 16 Jun 2020 10:00:29: 37000000 INFO @ Tue, 16 Jun 2020 10:00:32: 40000000 INFO @ Tue, 16 Jun 2020 10:00:35: 38000000 INFO @ Tue, 16 Jun 2020 10:00:39: 41000000 INFO @ Tue, 16 Jun 2020 10:00:42: 39000000 INFO @ Tue, 16 Jun 2020 10:00:45: 42000000 INFO @ Tue, 16 Jun 2020 10:00:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:00:48: 40000000 INFO @ Tue, 16 Jun 2020 10:00:52: 43000000 INFO @ Tue, 16 Jun 2020 10:00:53: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:00:53: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:00:53: #1 total tags in treatment: 20679171 INFO @ Tue, 16 Jun 2020 10:00:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:00:53: #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 10:00:54: #1 tags after filtering in treatment: 17174443 INFO @ Tue, 16 Jun 2020 10:00:54: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 16 Jun 2020 10:00:54: #1 finished! INFO @ Tue, 16 Jun 2020 10:00:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:00:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:00:54: 41000000 INFO @ Tue, 16 Jun 2020 10:00:55: #2 number of paired peaks: 681 WARNING @ Tue, 16 Jun 2020 10:00:55: Fewer paired peaks (681) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 681 pairs to build model! INFO @ Tue, 16 Jun 2020 10:00:55: start model_add_line... INFO @ Tue, 16 Jun 2020 10:00:55: start X-correlation... INFO @ Tue, 16 Jun 2020 10:00:55: end of X-cor INFO @ Tue, 16 Jun 2020 10:00:55: #2 finished! INFO @ Tue, 16 Jun 2020 10:00:55: #2 predicted fragment length is 198 bps INFO @ Tue, 16 Jun 2020 10:00:55: #2 alternative fragment length(s) may be 4,198 bps INFO @ Tue, 16 Jun 2020 10:00:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.10_model.r INFO @ Tue, 16 Jun 2020 10:00:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:00:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:01:00: 42000000 INFO @ Tue, 16 Jun 2020 10:01:06: 43000000 INFO @ Tue, 16 Jun 2020 10:01:07: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 10:01:07: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 10:01:07: #1 total tags in treatment: 20679171 INFO @ Tue, 16 Jun 2020 10:01:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:01:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:01:07: #1 tags after filtering in treatment: 17174443 INFO @ Tue, 16 Jun 2020 10:01:07: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 16 Jun 2020 10:01:07: #1 finished! INFO @ Tue, 16 Jun 2020 10:01:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:01:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:01:08: #2 number of paired peaks: 681 WARNING @ Tue, 16 Jun 2020 10:01:08: Fewer paired peaks (681) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 681 pairs to build model! INFO @ Tue, 16 Jun 2020 10:01:08: start model_add_line... INFO @ Tue, 16 Jun 2020 10:01:09: start X-correlation... INFO @ Tue, 16 Jun 2020 10:01:09: end of X-cor INFO @ Tue, 16 Jun 2020 10:01:09: #2 finished! INFO @ Tue, 16 Jun 2020 10:01:09: #2 predicted fragment length is 198 bps INFO @ Tue, 16 Jun 2020 10:01:09: #2 alternative fragment length(s) may be 4,198 bps INFO @ Tue, 16 Jun 2020 10:01:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.20_model.r INFO @ Tue, 16 Jun 2020 10:01:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:01:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:01:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:01:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:01:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.05_summits.bed INFO @ Tue, 16 Jun 2020 10:01:10: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4746 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:01:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:01:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:01:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:01:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:01:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.10_summits.bed INFO @ Tue, 16 Jun 2020 10:01:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2658 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:02:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:02:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:02:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733157/SRX3733157.20_summits.bed INFO @ Tue, 16 Jun 2020 10:02:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1212 records, 4 fields): 3 millis CompletedMACS2peakCalling