Job ID = 6367772 SRX = SRX4085342 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:36:29 prefetch.2.10.7: 1) Downloading 'SRR7167371'... 2020-06-15T23:36:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:03 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:03 prefetch.2.10.7: 1) 'SRR7167371' was downloaded successfully Read 26880650 spots for SRR7167371/SRR7167371.sra Written 26880650 spots for SRR7167371/SRR7167371.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: 00:21:57 26880650 reads; of these: 26880650 (100.00%) were paired; of these: 2023758 (7.53%) aligned concordantly 0 times 21727518 (80.83%) aligned concordantly exactly 1 time 3129374 (11.64%) aligned concordantly >1 times ---- 2023758 pairs aligned concordantly 0 times; of these: 188898 (9.33%) aligned discordantly 1 time ---- 1834860 pairs aligned 0 times concordantly or discordantly; of these: 3669720 mates make up the pairs; of these: 2073775 (56.51%) aligned 0 times 1316689 (35.88%) aligned exactly 1 time 279256 (7.61%) aligned >1 times 96.14% overall alignment rate Time searching: 00:21:57 Overall time: 00:21:57 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 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] 4638108 / 24987076 = 0.1856 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 09:28:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.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 09:28:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:40: 1000000 INFO @ Tue, 16 Jun 2020 09:28:45: 2000000 INFO @ Tue, 16 Jun 2020 09:28:51: 3000000 INFO @ Tue, 16 Jun 2020 09:28:56: 4000000 INFO @ Tue, 16 Jun 2020 09:29:02: 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 09:29:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.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 09:29:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:08: 6000000 INFO @ Tue, 16 Jun 2020 09:29:12: 1000000 INFO @ Tue, 16 Jun 2020 09:29:15: 7000000 INFO @ Tue, 16 Jun 2020 09:29:20: 2000000 INFO @ Tue, 16 Jun 2020 09:29:23: 8000000 INFO @ Tue, 16 Jun 2020 09:29:29: 3000000 INFO @ Tue, 16 Jun 2020 09:29:30: 9000000 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 09:29:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.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 09:29:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:37: 10000000 INFO @ Tue, 16 Jun 2020 09:29:37: 4000000 INFO @ Tue, 16 Jun 2020 09:29:42: 1000000 INFO @ Tue, 16 Jun 2020 09:29:44: 11000000 INFO @ Tue, 16 Jun 2020 09:29:45: 5000000 INFO @ Tue, 16 Jun 2020 09:29:49: 2000000 INFO @ Tue, 16 Jun 2020 09:29:52: 12000000 INFO @ Tue, 16 Jun 2020 09:29:54: 6000000 INFO @ Tue, 16 Jun 2020 09:29:57: 3000000 INFO @ Tue, 16 Jun 2020 09:30:00: 13000000 INFO @ Tue, 16 Jun 2020 09:30:02: 7000000 INFO @ Tue, 16 Jun 2020 09:30:04: 4000000 INFO @ Tue, 16 Jun 2020 09:30:07: 14000000 INFO @ Tue, 16 Jun 2020 09:30:10: 8000000 INFO @ Tue, 16 Jun 2020 09:30:12: 5000000 INFO @ Tue, 16 Jun 2020 09:30:15: 15000000 INFO @ Tue, 16 Jun 2020 09:30:18: 9000000 INFO @ Tue, 16 Jun 2020 09:30:20: 6000000 INFO @ Tue, 16 Jun 2020 09:30:22: 16000000 INFO @ Tue, 16 Jun 2020 09:30:26: 10000000 INFO @ Tue, 16 Jun 2020 09:30:27: 7000000 INFO @ Tue, 16 Jun 2020 09:30:30: 17000000 INFO @ Tue, 16 Jun 2020 09:30:34: 11000000 INFO @ Tue, 16 Jun 2020 09:30:35: 8000000 INFO @ Tue, 16 Jun 2020 09:30:38: 18000000 INFO @ Tue, 16 Jun 2020 09:30:42: 12000000 INFO @ Tue, 16 Jun 2020 09:30:42: 9000000 INFO @ Tue, 16 Jun 2020 09:30:45: 19000000 INFO @ Tue, 16 Jun 2020 09:30:50: 13000000 INFO @ Tue, 16 Jun 2020 09:30:50: 10000000 INFO @ Tue, 16 Jun 2020 09:30:53: 20000000 INFO @ Tue, 16 Jun 2020 09:30:58: 11000000 INFO @ Tue, 16 Jun 2020 09:30:58: 14000000 INFO @ Tue, 16 Jun 2020 09:31:00: 21000000 INFO @ Tue, 16 Jun 2020 09:31:05: 12000000 INFO @ Tue, 16 Jun 2020 09:31:06: 15000000 INFO @ Tue, 16 Jun 2020 09:31:08: 22000000 INFO @ Tue, 16 Jun 2020 09:31:13: 13000000 INFO @ Tue, 16 Jun 2020 09:31:14: 16000000 INFO @ Tue, 16 Jun 2020 09:31:15: 23000000 INFO @ Tue, 16 Jun 2020 09:31:20: 14000000 INFO @ Tue, 16 Jun 2020 09:31:22: 17000000 INFO @ Tue, 16 Jun 2020 09:31:23: 24000000 INFO @ Tue, 16 Jun 2020 09:31:28: 15000000 INFO @ Tue, 16 Jun 2020 09:31:30: 18000000 INFO @ Tue, 16 Jun 2020 09:31:31: 25000000 INFO @ Tue, 16 Jun 2020 09:31:36: 16000000 INFO @ Tue, 16 Jun 2020 09:31:38: 19000000 INFO @ Tue, 16 Jun 2020 09:31:38: 26000000 INFO @ Tue, 16 Jun 2020 09:31:43: 17000000 INFO @ Tue, 16 Jun 2020 09:31:46: 20000000 INFO @ Tue, 16 Jun 2020 09:31:46: 27000000 INFO @ Tue, 16 Jun 2020 09:31:51: 18000000 INFO @ Tue, 16 Jun 2020 09:31:54: 28000000 INFO @ Tue, 16 Jun 2020 09:31:54: 21000000 INFO @ Tue, 16 Jun 2020 09:31:58: 19000000 INFO @ Tue, 16 Jun 2020 09:32:01: 29000000 INFO @ Tue, 16 Jun 2020 09:32:02: 22000000 INFO @ Tue, 16 Jun 2020 09:32:06: 20000000 INFO @ Tue, 16 Jun 2020 09:32:09: 30000000 INFO @ Tue, 16 Jun 2020 09:32:10: 23000000 INFO @ Tue, 16 Jun 2020 09:32:13: 21000000 INFO @ Tue, 16 Jun 2020 09:32:16: 31000000 INFO @ Tue, 16 Jun 2020 09:32:18: 24000000 INFO @ Tue, 16 Jun 2020 09:32:21: 22000000 INFO @ Tue, 16 Jun 2020 09:32:24: 32000000 INFO @ Tue, 16 Jun 2020 09:32:26: 25000000 INFO @ Tue, 16 Jun 2020 09:32:28: 23000000 INFO @ Tue, 16 Jun 2020 09:32:31: 33000000 INFO @ Tue, 16 Jun 2020 09:32:34: 26000000 INFO @ Tue, 16 Jun 2020 09:32:36: 24000000 INFO @ Tue, 16 Jun 2020 09:32:39: 34000000 INFO @ Tue, 16 Jun 2020 09:32:41: 27000000 INFO @ Tue, 16 Jun 2020 09:32:43: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:32:46: 35000000 INFO @ Tue, 16 Jun 2020 09:32:48: 28000000 INFO @ Tue, 16 Jun 2020 09:32:51: 26000000 INFO @ Tue, 16 Jun 2020 09:32:53: 36000000 INFO @ Tue, 16 Jun 2020 09:32:56: 29000000 INFO @ Tue, 16 Jun 2020 09:32:59: 27000000 INFO @ Tue, 16 Jun 2020 09:33:01: 37000000 INFO @ Tue, 16 Jun 2020 09:33:03: 30000000 INFO @ Tue, 16 Jun 2020 09:33:07: 28000000 INFO @ Tue, 16 Jun 2020 09:33:08: 38000000 INFO @ Tue, 16 Jun 2020 09:33:10: 31000000 INFO @ Tue, 16 Jun 2020 09:33:15: 39000000 INFO @ Tue, 16 Jun 2020 09:33:15: 29000000 INFO @ Tue, 16 Jun 2020 09:33:17: 32000000 INFO @ Tue, 16 Jun 2020 09:33:22: 40000000 INFO @ Tue, 16 Jun 2020 09:33:23: 30000000 INFO @ Tue, 16 Jun 2020 09:33:24: 33000000 INFO @ Tue, 16 Jun 2020 09:33:29: 41000000 INFO @ Tue, 16 Jun 2020 09:33:31: 31000000 INFO @ Tue, 16 Jun 2020 09:33:32: 34000000 INFO @ Tue, 16 Jun 2020 09:33:36: 42000000 INFO @ Tue, 16 Jun 2020 09:33:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:33:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:33:39: #1 total tags in treatment: 20233536 INFO @ Tue, 16 Jun 2020 09:33:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:39: #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 09:33:39: 32000000 INFO @ Tue, 16 Jun 2020 09:33:39: #1 tags after filtering in treatment: 17101636 INFO @ Tue, 16 Jun 2020 09:33:39: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:33:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:40: 35000000 INFO @ Tue, 16 Jun 2020 09:33:40: #2 number of paired peaks: 174 WARNING @ Tue, 16 Jun 2020 09:33:40: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:40: #2 predicted fragment length is 116 bps INFO @ Tue, 16 Jun 2020 09:33:40: #2 alternative fragment length(s) may be 2,85,116,138 bps INFO @ Tue, 16 Jun 2020 09:33:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.05_model.r INFO @ Tue, 16 Jun 2020 09:33:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:47: 33000000 INFO @ Tue, 16 Jun 2020 09:33:48: 36000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:33:55: 34000000 INFO @ Tue, 16 Jun 2020 09:33:56: 37000000 INFO @ Tue, 16 Jun 2020 09:34:02: 35000000 INFO @ Tue, 16 Jun 2020 09:34:04: 38000000 INFO @ Tue, 16 Jun 2020 09:34:10: 36000000 INFO @ Tue, 16 Jun 2020 09:34:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:12: 39000000 INFO @ Tue, 16 Jun 2020 09:34:17: 37000000 INFO @ Tue, 16 Jun 2020 09:34:20: 40000000 INFO @ Tue, 16 Jun 2020 09:34:25: 38000000 INFO @ Tue, 16 Jun 2020 09:34:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.05_summits.bed INFO @ Tue, 16 Jun 2020 09:34:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2086 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:34:28: 41000000 INFO @ Tue, 16 Jun 2020 09:34:33: 39000000 INFO @ Tue, 16 Jun 2020 09:34:35: 42000000 INFO @ Tue, 16 Jun 2020 09:34:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:34:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:34:38: #1 total tags in treatment: 20233536 INFO @ Tue, 16 Jun 2020 09:34:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:38: #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 09:34:39: #1 tags after filtering in treatment: 17101636 INFO @ Tue, 16 Jun 2020 09:34:39: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:34:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:40: 40000000 INFO @ Tue, 16 Jun 2020 09:34:40: #2 number of paired peaks: 174 WARNING @ Tue, 16 Jun 2020 09:34:40: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:40: #2 predicted fragment length is 116 bps INFO @ Tue, 16 Jun 2020 09:34:40: #2 alternative fragment length(s) may be 2,85,116,138 bps INFO @ Tue, 16 Jun 2020 09:34:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.10_model.r INFO @ Tue, 16 Jun 2020 09:34:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:46: 41000000 INFO @ Tue, 16 Jun 2020 09:34:51: 42000000 INFO @ Tue, 16 Jun 2020 09:34:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:34:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:34:54: #1 total tags in treatment: 20233536 INFO @ Tue, 16 Jun 2020 09:34:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:54: #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 09:34:54: #1 tags after filtering in treatment: 17101636 INFO @ Tue, 16 Jun 2020 09:34:54: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:34:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:55: #2 number of paired peaks: 174 WARNING @ Tue, 16 Jun 2020 09:34:55: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:55: #2 predicted fragment length is 116 bps INFO @ Tue, 16 Jun 2020 09:34:55: #2 alternative fragment length(s) may be 2,85,116,138 bps INFO @ Tue, 16 Jun 2020 09:34:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.20_model.r INFO @ Tue, 16 Jun 2020 09:34:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.10_summits.bed INFO @ Tue, 16 Jun 2020 09:35:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1151 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085342/SRX4085342.20_summits.bed INFO @ Tue, 16 Jun 2020 09:35:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (532 records, 4 fields): 2 millis CompletedMACS2peakCalling