Job ID = 6367659 SRX = SRX3733153 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:32:05 prefetch.2.10.7: 1) Downloading 'SRR6760666'... 2020-06-15T23:32:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:46 prefetch.2.10.7: 1) 'SRR6760666' was downloaded successfully 2020-06-15T23:41:46 prefetch.2.10.7: 'SRR6760666' has 0 unresolved dependencies Read 28529693 spots for SRR6760666/SRR6760666.sra Written 28529693 spots for SRR6760666/SRR6760666.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: 00:32:27 28529693 reads; of these: 28529693 (100.00%) were paired; of these: 2540166 (8.90%) aligned concordantly 0 times 24053155 (84.31%) aligned concordantly exactly 1 time 1936372 (6.79%) aligned concordantly >1 times ---- 2540166 pairs aligned concordantly 0 times; of these: 1087646 (42.82%) aligned discordantly 1 time ---- 1452520 pairs aligned 0 times concordantly or discordantly; of these: 2905040 mates make up the pairs; of these: 1958510 (67.42%) aligned 0 times 650465 (22.39%) aligned exactly 1 time 296065 (10.19%) aligned >1 times 96.57% overall alignment rate Time searching: 00:32:27 Overall time: 00:32:27 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] 10373907 / 26812686 = 0.3869 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 09:33:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.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 09:33:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:25: 1000000 INFO @ Tue, 16 Jun 2020 09:33:32: 2000000 INFO @ Tue, 16 Jun 2020 09:33:39: 3000000 INFO @ Tue, 16 Jun 2020 09:33:46: 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 09:33:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.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 09:33:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:54: 5000000 INFO @ Tue, 16 Jun 2020 09:33:59: 1000000 INFO @ Tue, 16 Jun 2020 09:34:04: 6000000 INFO @ Tue, 16 Jun 2020 09:34:09: 2000000 INFO @ Tue, 16 Jun 2020 09:34:13: 7000000 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 09:34:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.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 09:34:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:19: 3000000 INFO @ Tue, 16 Jun 2020 09:34:22: 8000000 INFO @ Tue, 16 Jun 2020 09:34:28: 1000000 INFO @ Tue, 16 Jun 2020 09:34:29: 4000000 INFO @ Tue, 16 Jun 2020 09:34:32: 9000000 INFO @ Tue, 16 Jun 2020 09:34:38: 2000000 INFO @ Tue, 16 Jun 2020 09:34:39: 5000000 INFO @ Tue, 16 Jun 2020 09:34:42: 10000000 INFO @ Tue, 16 Jun 2020 09:34:48: 3000000 INFO @ Tue, 16 Jun 2020 09:34:50: 6000000 INFO @ Tue, 16 Jun 2020 09:34:52: 11000000 INFO @ Tue, 16 Jun 2020 09:34:58: 4000000 INFO @ Tue, 16 Jun 2020 09:35:00: 7000000 INFO @ Tue, 16 Jun 2020 09:35:01: 12000000 INFO @ Tue, 16 Jun 2020 09:35:08: 5000000 INFO @ Tue, 16 Jun 2020 09:35:10: 8000000 INFO @ Tue, 16 Jun 2020 09:35:11: 13000000 INFO @ Tue, 16 Jun 2020 09:35:18: 6000000 INFO @ Tue, 16 Jun 2020 09:35:21: 9000000 INFO @ Tue, 16 Jun 2020 09:35:21: 14000000 INFO @ Tue, 16 Jun 2020 09:35:28: 7000000 INFO @ Tue, 16 Jun 2020 09:35:31: 10000000 INFO @ Tue, 16 Jun 2020 09:35:31: 15000000 INFO @ Tue, 16 Jun 2020 09:35:38: 8000000 INFO @ Tue, 16 Jun 2020 09:35:41: 16000000 INFO @ Tue, 16 Jun 2020 09:35:41: 11000000 INFO @ Tue, 16 Jun 2020 09:35:48: 9000000 INFO @ Tue, 16 Jun 2020 09:35:51: 17000000 INFO @ Tue, 16 Jun 2020 09:35:52: 12000000 INFO @ Tue, 16 Jun 2020 09:35:58: 10000000 INFO @ Tue, 16 Jun 2020 09:36:01: 18000000 INFO @ Tue, 16 Jun 2020 09:36:02: 13000000 INFO @ Tue, 16 Jun 2020 09:36:08: 11000000 INFO @ Tue, 16 Jun 2020 09:36:11: 19000000 INFO @ Tue, 16 Jun 2020 09:36:12: 14000000 INFO @ Tue, 16 Jun 2020 09:36:18: 12000000 INFO @ Tue, 16 Jun 2020 09:36:21: 20000000 INFO @ Tue, 16 Jun 2020 09:36:23: 15000000 INFO @ Tue, 16 Jun 2020 09:36:28: 13000000 INFO @ Tue, 16 Jun 2020 09:36:30: 21000000 INFO @ Tue, 16 Jun 2020 09:36:33: 16000000 INFO @ Tue, 16 Jun 2020 09:36:38: 14000000 INFO @ Tue, 16 Jun 2020 09:36:40: 22000000 INFO @ Tue, 16 Jun 2020 09:36:43: 17000000 INFO @ Tue, 16 Jun 2020 09:36:48: 15000000 INFO @ Tue, 16 Jun 2020 09:36:50: 23000000 INFO @ Tue, 16 Jun 2020 09:36:54: 18000000 INFO @ Tue, 16 Jun 2020 09:36:58: 16000000 INFO @ Tue, 16 Jun 2020 09:36:59: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:37:04: 19000000 INFO @ Tue, 16 Jun 2020 09:37:07: 17000000 INFO @ Tue, 16 Jun 2020 09:37:09: 25000000 INFO @ Tue, 16 Jun 2020 09:37:15: 20000000 INFO @ Tue, 16 Jun 2020 09:37:17: 18000000 INFO @ Tue, 16 Jun 2020 09:37:19: 26000000 INFO @ Tue, 16 Jun 2020 09:37:26: 21000000 INFO @ Tue, 16 Jun 2020 09:37:27: 19000000 INFO @ Tue, 16 Jun 2020 09:37:29: 27000000 INFO @ Tue, 16 Jun 2020 09:37:37: 22000000 INFO @ Tue, 16 Jun 2020 09:37:37: 20000000 INFO @ Tue, 16 Jun 2020 09:37:39: 28000000 INFO @ Tue, 16 Jun 2020 09:37:47: 21000000 INFO @ Tue, 16 Jun 2020 09:37:48: 23000000 INFO @ Tue, 16 Jun 2020 09:37:49: 29000000 INFO @ Tue, 16 Jun 2020 09:37:57: 22000000 INFO @ Tue, 16 Jun 2020 09:37:58: 24000000 INFO @ Tue, 16 Jun 2020 09:37:59: 30000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:38:07: 23000000 INFO @ Tue, 16 Jun 2020 09:38:09: 31000000 INFO @ Tue, 16 Jun 2020 09:38:09: 25000000 INFO @ Tue, 16 Jun 2020 09:38:17: 24000000 INFO @ Tue, 16 Jun 2020 09:38:19: 32000000 INFO @ Tue, 16 Jun 2020 09:38:20: 26000000 INFO @ Tue, 16 Jun 2020 09:38:27: 25000000 INFO @ Tue, 16 Jun 2020 09:38:28: 33000000 INFO @ Tue, 16 Jun 2020 09:38:31: 27000000 INFO @ Tue, 16 Jun 2020 09:38:36: 26000000 INFO @ Tue, 16 Jun 2020 09:38:38: 34000000 INFO @ Tue, 16 Jun 2020 09:38:41: 28000000 INFO @ Tue, 16 Jun 2020 09:38:42: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:38:42: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:38:42: #1 total tags in treatment: 15841422 INFO @ Tue, 16 Jun 2020 09:38:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:42: #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 09:38:42: #1 tags after filtering in treatment: 13702776 INFO @ Tue, 16 Jun 2020 09:38:42: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:38:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:43: #2 number of paired peaks: 422 WARNING @ Tue, 16 Jun 2020 09:38:43: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Tue, 16 Jun 2020 09:38:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:43: #2 predicted fragment length is 192 bps INFO @ Tue, 16 Jun 2020 09:38:43: #2 alternative fragment length(s) may be 4,192 bps INFO @ Tue, 16 Jun 2020 09:38:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.05_model.r INFO @ Tue, 16 Jun 2020 09:38:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:38:46: 27000000 INFO @ Tue, 16 Jun 2020 09:38:52: 29000000 INFO @ Tue, 16 Jun 2020 09:38:56: 28000000 INFO @ Tue, 16 Jun 2020 09:39:02: 30000000 INFO @ Tue, 16 Jun 2020 09:39:05: 29000000 INFO @ Tue, 16 Jun 2020 09:39:13: 31000000 INFO @ Tue, 16 Jun 2020 09:39:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:15: 30000000 INFO @ Tue, 16 Jun 2020 09:39:23: 32000000 INFO @ Tue, 16 Jun 2020 09:39:24: 31000000 INFO @ Tue, 16 Jun 2020 09:39:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.05_summits.bed INFO @ Tue, 16 Jun 2020 09:39:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3630 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:39:33: 33000000 INFO @ Tue, 16 Jun 2020 09:39:34: 32000000 INFO @ Tue, 16 Jun 2020 09:39:43: 33000000 INFO @ Tue, 16 Jun 2020 09:39:44: 34000000 INFO @ Tue, 16 Jun 2020 09:39:47: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:39:47: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:39:47: #1 total tags in treatment: 15841422 INFO @ Tue, 16 Jun 2020 09:39:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:47: #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 09:39:48: #1 tags after filtering in treatment: 13702776 INFO @ Tue, 16 Jun 2020 09:39:48: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:39:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:49: #2 number of paired peaks: 422 WARNING @ Tue, 16 Jun 2020 09:39:49: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:49: #2 predicted fragment length is 192 bps INFO @ Tue, 16 Jun 2020 09:39:49: #2 alternative fragment length(s) may be 4,192 bps INFO @ Tue, 16 Jun 2020 09:39:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.10_model.r INFO @ Tue, 16 Jun 2020 09:39:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:52: 34000000 INFO @ Tue, 16 Jun 2020 09:39:54: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:39:54: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:39:54: #1 total tags in treatment: 15841422 INFO @ Tue, 16 Jun 2020 09:39:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:54: #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 09:39:55: #1 tags after filtering in treatment: 13702776 INFO @ Tue, 16 Jun 2020 09:39:55: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:39:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:56: #2 number of paired peaks: 422 WARNING @ Tue, 16 Jun 2020 09:39:56: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:56: #2 predicted fragment length is 192 bps INFO @ Tue, 16 Jun 2020 09:39:56: #2 alternative fragment length(s) may be 4,192 bps INFO @ Tue, 16 Jun 2020 09:39:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.20_model.r INFO @ Tue, 16 Jun 2020 09:39:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.10_summits.bed INFO @ Tue, 16 Jun 2020 09:40:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2000 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733153/SRX3733153.20_summits.bed INFO @ Tue, 16 Jun 2020 09:40:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (840 records, 4 fields): 2 millis CompletedMACS2peakCalling