Job ID = 6367792 SRX = SRX4085360 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:32:20 prefetch.2.10.7: 1) Downloading 'SRR7167389'... 2020-06-15T23:32:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:51 prefetch.2.10.7: 1) 'SRR7167389' was downloaded successfully Read 19703192 spots for SRR7167389/SRR7167389.sra Written 19703192 spots for SRR7167389/SRR7167389.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: 00:16:03 19703192 reads; of these: 19703192 (100.00%) were paired; of these: 1150149 (5.84%) aligned concordantly 0 times 16150491 (81.97%) aligned concordantly exactly 1 time 2402552 (12.19%) aligned concordantly >1 times ---- 1150149 pairs aligned concordantly 0 times; of these: 556153 (48.35%) aligned discordantly 1 time ---- 593996 pairs aligned 0 times concordantly or discordantly; of these: 1187992 mates make up the pairs; of these: 529295 (44.55%) aligned 0 times 385823 (32.48%) aligned exactly 1 time 272874 (22.97%) aligned >1 times 98.66% overall alignment rate Time searching: 00:16:03 Overall time: 00:16:03 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 16 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] 2387851 / 18667473 = 0.1279 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 09:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.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 09:07:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:45: 1000000 INFO @ Tue, 16 Jun 2020 09:07:50: 2000000 INFO @ Tue, 16 Jun 2020 09:07:55: 3000000 INFO @ Tue, 16 Jun 2020 09:08:01: 4000000 INFO @ Tue, 16 Jun 2020 09:08:06: 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 09:08:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.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 09:08:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:12: 6000000 INFO @ Tue, 16 Jun 2020 09:08:15: 1000000 INFO @ Tue, 16 Jun 2020 09:08:17: 7000000 INFO @ Tue, 16 Jun 2020 09:08:21: 2000000 INFO @ Tue, 16 Jun 2020 09:08:23: 8000000 INFO @ Tue, 16 Jun 2020 09:08:26: 3000000 INFO @ Tue, 16 Jun 2020 09:08:28: 9000000 INFO @ Tue, 16 Jun 2020 09:08:31: 4000000 INFO @ Tue, 16 Jun 2020 09:08:34: 10000000 INFO @ Tue, 16 Jun 2020 09:08:37: 5000000 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 09:08:40: 11000000 INFO @ Tue, 16 Jun 2020 09:08:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.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 09:08:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:42: 6000000 INFO @ Tue, 16 Jun 2020 09:08:45: 12000000 INFO @ Tue, 16 Jun 2020 09:08:45: 1000000 INFO @ Tue, 16 Jun 2020 09:08:47: 7000000 INFO @ Tue, 16 Jun 2020 09:08:51: 2000000 INFO @ Tue, 16 Jun 2020 09:08:51: 13000000 INFO @ Tue, 16 Jun 2020 09:08:53: 8000000 INFO @ Tue, 16 Jun 2020 09:08:56: 3000000 INFO @ Tue, 16 Jun 2020 09:08:57: 14000000 INFO @ Tue, 16 Jun 2020 09:08:59: 9000000 INFO @ Tue, 16 Jun 2020 09:09:02: 4000000 INFO @ Tue, 16 Jun 2020 09:09:04: 15000000 INFO @ Tue, 16 Jun 2020 09:09:05: 10000000 INFO @ Tue, 16 Jun 2020 09:09:07: 5000000 INFO @ Tue, 16 Jun 2020 09:09:10: 11000000 INFO @ Tue, 16 Jun 2020 09:09:11: 16000000 INFO @ Tue, 16 Jun 2020 09:09:13: 6000000 INFO @ Tue, 16 Jun 2020 09:09:16: 12000000 INFO @ Tue, 16 Jun 2020 09:09:18: 17000000 INFO @ Tue, 16 Jun 2020 09:09:18: 7000000 INFO @ Tue, 16 Jun 2020 09:09:22: 13000000 INFO @ Tue, 16 Jun 2020 09:09:24: 8000000 INFO @ Tue, 16 Jun 2020 09:09:24: 18000000 INFO @ Tue, 16 Jun 2020 09:09:28: 14000000 INFO @ Tue, 16 Jun 2020 09:09:29: 9000000 INFO @ Tue, 16 Jun 2020 09:09:31: 19000000 INFO @ Tue, 16 Jun 2020 09:09:34: 15000000 INFO @ Tue, 16 Jun 2020 09:09:35: 10000000 INFO @ Tue, 16 Jun 2020 09:09:38: 20000000 INFO @ Tue, 16 Jun 2020 09:09:40: 16000000 INFO @ Tue, 16 Jun 2020 09:09:40: 11000000 INFO @ Tue, 16 Jun 2020 09:09:45: 21000000 INFO @ Tue, 16 Jun 2020 09:09:45: 17000000 INFO @ Tue, 16 Jun 2020 09:09:46: 12000000 INFO @ Tue, 16 Jun 2020 09:09:51: 18000000 INFO @ Tue, 16 Jun 2020 09:09:51: 13000000 INFO @ Tue, 16 Jun 2020 09:09:52: 22000000 INFO @ Tue, 16 Jun 2020 09:09:57: 14000000 INFO @ Tue, 16 Jun 2020 09:09:57: 19000000 INFO @ Tue, 16 Jun 2020 09:09:58: 23000000 INFO @ Tue, 16 Jun 2020 09:10:02: 15000000 INFO @ Tue, 16 Jun 2020 09:10:03: 20000000 INFO @ Tue, 16 Jun 2020 09:10:05: 24000000 INFO @ Tue, 16 Jun 2020 09:10:08: 16000000 INFO @ Tue, 16 Jun 2020 09:10:09: 21000000 INFO @ Tue, 16 Jun 2020 09:10:12: 25000000 INFO @ Tue, 16 Jun 2020 09:10:13: 17000000 INFO @ Tue, 16 Jun 2020 09:10:15: 22000000 INFO @ Tue, 16 Jun 2020 09:10:19: 18000000 INFO @ Tue, 16 Jun 2020 09:10:19: 26000000 INFO @ Tue, 16 Jun 2020 09:10:21: 23000000 INFO @ Tue, 16 Jun 2020 09:10:24: 19000000 INFO @ Tue, 16 Jun 2020 09:10:26: 27000000 INFO @ Tue, 16 Jun 2020 09:10:26: 24000000 INFO @ Tue, 16 Jun 2020 09:10:30: 20000000 INFO @ Tue, 16 Jun 2020 09:10:32: 25000000 INFO @ Tue, 16 Jun 2020 09:10:33: 28000000 INFO @ Tue, 16 Jun 2020 09:10:35: 21000000 INFO @ Tue, 16 Jun 2020 09:10:38: 26000000 INFO @ Tue, 16 Jun 2020 09:10:40: 29000000 INFO @ Tue, 16 Jun 2020 09:10:41: 22000000 INFO @ Tue, 16 Jun 2020 09:10:44: 27000000 INFO @ Tue, 16 Jun 2020 09:10:46: 23000000 INFO @ Tue, 16 Jun 2020 09:10:47: 30000000 INFO @ Tue, 16 Jun 2020 09:10:49: 28000000 INFO @ Tue, 16 Jun 2020 09:10:52: 24000000 INFO @ Tue, 16 Jun 2020 09:10:54: 31000000 INFO @ Tue, 16 Jun 2020 09:10:55: 29000000 INFO @ Tue, 16 Jun 2020 09:10:57: 25000000 INFO @ Tue, 16 Jun 2020 09:11:01: 32000000 INFO @ Tue, 16 Jun 2020 09:11:01: 30000000 INFO @ Tue, 16 Jun 2020 09:11:03: 26000000 INFO @ Tue, 16 Jun 2020 09:11:06: 31000000 INFO @ Tue, 16 Jun 2020 09:11:08: 33000000 INFO @ Tue, 16 Jun 2020 09:11:08: 27000000 INFO @ Tue, 16 Jun 2020 09:11:12: 32000000 INFO @ Tue, 16 Jun 2020 09:11:14: 28000000 INFO @ Tue, 16 Jun 2020 09:11:14: 34000000 INFO @ Tue, 16 Jun 2020 09:11:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:11:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:11:15: #1 total tags in treatment: 16176831 INFO @ Tue, 16 Jun 2020 09:11:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:15: #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 09:11:15: #1 tags after filtering in treatment: 13850446 INFO @ Tue, 16 Jun 2020 09:11:15: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:11:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:16: #2 number of paired peaks: 214 WARNING @ Tue, 16 Jun 2020 09:11:16: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:17: #2 predicted fragment length is 104 bps INFO @ Tue, 16 Jun 2020 09:11:17: #2 alternative fragment length(s) may be 3,78,104,129,148 bps INFO @ Tue, 16 Jun 2020 09:11:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.05_model.r INFO @ Tue, 16 Jun 2020 09:11:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:17: 33000000 INFO @ Tue, 16 Jun 2020 09:11:19: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:11:23: 34000000 INFO @ Tue, 16 Jun 2020 09:11:24: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:11:24: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:11:24: #1 total tags in treatment: 16176831 INFO @ Tue, 16 Jun 2020 09:11:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:24: #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 09:11:24: #1 tags after filtering in treatment: 13850446 INFO @ Tue, 16 Jun 2020 09:11:24: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:11:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:24: 30000000 INFO @ Tue, 16 Jun 2020 09:11:25: #2 number of paired peaks: 214 WARNING @ Tue, 16 Jun 2020 09:11:25: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:25: #2 predicted fragment length is 104 bps INFO @ Tue, 16 Jun 2020 09:11:25: #2 alternative fragment length(s) may be 3,78,104,129,148 bps INFO @ Tue, 16 Jun 2020 09:11:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.10_model.r INFO @ Tue, 16 Jun 2020 09:11:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:30: 31000000 INFO @ Tue, 16 Jun 2020 09:11:35: 32000000 INFO @ Tue, 16 Jun 2020 09:11:40: 33000000 INFO @ Tue, 16 Jun 2020 09:11:46: 34000000 INFO @ Tue, 16 Jun 2020 09:11:46: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:11:46: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:11:46: #1 total tags in treatment: 16176831 INFO @ Tue, 16 Jun 2020 09:11:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:46: #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 09:11:47: #1 tags after filtering in treatment: 13850446 INFO @ Tue, 16 Jun 2020 09:11:47: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:11:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:48: #2 number of paired peaks: 214 WARNING @ Tue, 16 Jun 2020 09:11:48: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:48: #2 predicted fragment length is 104 bps INFO @ Tue, 16 Jun 2020 09:11:48: #2 alternative fragment length(s) may be 3,78,104,129,148 bps INFO @ Tue, 16 Jun 2020 09:11:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.20_model.r INFO @ Tue, 16 Jun 2020 09:11:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2108 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (989 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:12:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085360/SRX4085360.20_summits.bed INFO @ Tue, 16 Jun 2020 09:12:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (295 records, 4 fields): 2 millis CompletedMACS2peakCalling