Job ID = 6366358 SRX = SRX1353657 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T22:47:56 prefetch.2.10.7: 1) Downloading 'SRR2722811'... 2020-06-15T22:47:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:49:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:49:42 prefetch.2.10.7: 1) 'SRR2722811' was downloaded successfully Read 13019307 spots for SRR2722811/SRR2722811.sra Written 13019307 spots for SRR2722811/SRR2722811.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: 00:11:33 13019307 reads; of these: 13019307 (100.00%) were paired; of these: 536206 (4.12%) aligned concordantly 0 times 10586530 (81.31%) aligned concordantly exactly 1 time 1896571 (14.57%) aligned concordantly >1 times ---- 536206 pairs aligned concordantly 0 times; of these: 284310 (53.02%) aligned discordantly 1 time ---- 251896 pairs aligned 0 times concordantly or discordantly; of these: 503792 mates make up the pairs; of these: 233800 (46.41%) aligned 0 times 147901 (29.36%) aligned exactly 1 time 122091 (24.23%) aligned >1 times 99.10% overall alignment rate Time searching: 00:11:33 Overall time: 00:11:33 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 12 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] 159215 / 12661341 = 0.0126 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 08:10:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.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 08:10:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:21: 1000000 INFO @ Tue, 16 Jun 2020 08:10:26: 2000000 INFO @ Tue, 16 Jun 2020 08:10:30: 3000000 INFO @ Tue, 16 Jun 2020 08:10:35: 4000000 INFO @ Tue, 16 Jun 2020 08:10:39: 5000000 INFO @ Tue, 16 Jun 2020 08:10:43: 6000000 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 08:10:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.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 08:10:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:47: 7000000 INFO @ Tue, 16 Jun 2020 08:10:52: 8000000 INFO @ Tue, 16 Jun 2020 08:10:52: 1000000 INFO @ Tue, 16 Jun 2020 08:10:56: 9000000 INFO @ Tue, 16 Jun 2020 08:10:57: 2000000 INFO @ Tue, 16 Jun 2020 08:11:01: 10000000 INFO @ Tue, 16 Jun 2020 08:11:03: 3000000 INFO @ Tue, 16 Jun 2020 08:11:06: 11000000 INFO @ Tue, 16 Jun 2020 08:11:08: 4000000 INFO @ Tue, 16 Jun 2020 08:11:10: 12000000 INFO @ Tue, 16 Jun 2020 08:11:13: 5000000 INFO @ Tue, 16 Jun 2020 08:11:15: 13000000 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 08:11:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.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 08:11:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:19: 6000000 INFO @ Tue, 16 Jun 2020 08:11:19: 14000000 INFO @ Tue, 16 Jun 2020 08:11:22: 1000000 INFO @ Tue, 16 Jun 2020 08:11:24: 7000000 INFO @ Tue, 16 Jun 2020 08:11:24: 15000000 INFO @ Tue, 16 Jun 2020 08:11:28: 2000000 INFO @ Tue, 16 Jun 2020 08:11:28: 16000000 INFO @ Tue, 16 Jun 2020 08:11:29: 8000000 INFO @ Tue, 16 Jun 2020 08:11:33: 3000000 INFO @ Tue, 16 Jun 2020 08:11:33: 17000000 INFO @ Tue, 16 Jun 2020 08:11:35: 9000000 INFO @ Tue, 16 Jun 2020 08:11:38: 18000000 INFO @ Tue, 16 Jun 2020 08:11:38: 4000000 INFO @ Tue, 16 Jun 2020 08:11:40: 10000000 INFO @ Tue, 16 Jun 2020 08:11:42: 19000000 INFO @ Tue, 16 Jun 2020 08:11:44: 5000000 INFO @ Tue, 16 Jun 2020 08:11:46: 11000000 INFO @ Tue, 16 Jun 2020 08:11:47: 20000000 INFO @ Tue, 16 Jun 2020 08:11:49: 6000000 INFO @ Tue, 16 Jun 2020 08:11:51: 12000000 INFO @ Tue, 16 Jun 2020 08:11:52: 21000000 INFO @ Tue, 16 Jun 2020 08:11:55: 7000000 INFO @ Tue, 16 Jun 2020 08:11:56: 22000000 INFO @ Tue, 16 Jun 2020 08:11:57: 13000000 INFO @ Tue, 16 Jun 2020 08:12:00: 8000000 INFO @ Tue, 16 Jun 2020 08:12:01: 23000000 INFO @ Tue, 16 Jun 2020 08:12:02: 14000000 INFO @ Tue, 16 Jun 2020 08:12:05: 24000000 INFO @ Tue, 16 Jun 2020 08:12:06: 9000000 INFO @ Tue, 16 Jun 2020 08:12:08: 15000000 INFO @ Tue, 16 Jun 2020 08:12:10: 25000000 INFO @ Tue, 16 Jun 2020 08:12:11: 10000000 INFO @ Tue, 16 Jun 2020 08:12:12: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:12:12: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:12:12: #1 total tags in treatment: 12324680 INFO @ Tue, 16 Jun 2020 08:12:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:12: #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 08:12:12: #1 tags after filtering in treatment: 11402560 INFO @ Tue, 16 Jun 2020 08:12:12: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 08:12:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:13: #2 number of paired peaks: 328 WARNING @ Tue, 16 Jun 2020 08:12:13: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:13: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 08:12:13: #2 alternative fragment length(s) may be 4,170 bps INFO @ Tue, 16 Jun 2020 08:12:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.05_model.r INFO @ Tue, 16 Jun 2020 08:12:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:14: 16000000 INFO @ Tue, 16 Jun 2020 08:12:17: 11000000 INFO @ Tue, 16 Jun 2020 08:12:19: 17000000 INFO @ Tue, 16 Jun 2020 08:12:23: 12000000 INFO @ Tue, 16 Jun 2020 08:12:25: 18000000 INFO @ Tue, 16 Jun 2020 08:12:28: 13000000 INFO @ Tue, 16 Jun 2020 08:12:30: 19000000 INFO @ Tue, 16 Jun 2020 08:12:34: 14000000 INFO @ Tue, 16 Jun 2020 08:12:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:36: 20000000 INFO @ Tue, 16 Jun 2020 08:12:40: 15000000 INFO @ Tue, 16 Jun 2020 08:12:42: 21000000 INFO @ Tue, 16 Jun 2020 08:12:46: 16000000 INFO @ Tue, 16 Jun 2020 08:12:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.05_summits.bed INFO @ Tue, 16 Jun 2020 08:12:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (712 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:12:48: 22000000 INFO @ Tue, 16 Jun 2020 08:12:52: 17000000 INFO @ Tue, 16 Jun 2020 08:12:53: 23000000 INFO @ Tue, 16 Jun 2020 08:12:57: 18000000 INFO @ Tue, 16 Jun 2020 08:12:59: 24000000 INFO @ Tue, 16 Jun 2020 08:13:03: 19000000 INFO @ Tue, 16 Jun 2020 08:13:05: 25000000 INFO @ Tue, 16 Jun 2020 08:13:08: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:13:08: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:13:08: #1 total tags in treatment: 12324680 INFO @ Tue, 16 Jun 2020 08:13:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:08: #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 08:13:08: #1 tags after filtering in treatment: 11402560 INFO @ Tue, 16 Jun 2020 08:13:08: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 08:13:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:09: #2 number of paired peaks: 328 WARNING @ Tue, 16 Jun 2020 08:13:09: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:09: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 08:13:09: #2 alternative fragment length(s) may be 4,170 bps INFO @ Tue, 16 Jun 2020 08:13:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.10_model.r INFO @ Tue, 16 Jun 2020 08:13:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:09: 20000000 INFO @ Tue, 16 Jun 2020 08:13:15: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:13:20: 22000000 INFO @ Tue, 16 Jun 2020 08:13:26: 23000000 INFO @ Tue, 16 Jun 2020 08:13:32: 24000000 INFO @ Tue, 16 Jun 2020 08:13:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:37: 25000000 INFO @ Tue, 16 Jun 2020 08:13:40: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:13:40: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:13:40: #1 total tags in treatment: 12324680 INFO @ Tue, 16 Jun 2020 08:13:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:40: #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 08:13:40: #1 tags after filtering in treatment: 11402560 INFO @ Tue, 16 Jun 2020 08:13:40: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 08:13:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:41: #2 number of paired peaks: 328 WARNING @ Tue, 16 Jun 2020 08:13:41: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:41: #2 predicted fragment length is 170 bps INFO @ Tue, 16 Jun 2020 08:13:41: #2 alternative fragment length(s) may be 4,170 bps INFO @ Tue, 16 Jun 2020 08:13:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.20_model.r INFO @ Tue, 16 Jun 2020 08:13:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.10_summits.bed INFO @ Tue, 16 Jun 2020 08:13:45: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (295 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:14:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353657/SRX1353657.20_summits.bed INFO @ Tue, 16 Jun 2020 08:14:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (185 records, 4 fields): 1 millis CompletedMACS2peakCalling