Job ID = 6507721 SRX = SRX1353660 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:44:31 prefetch.2.10.7: 1) Downloading 'SRR2722814'... 2020-06-26T13:44:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:46:29 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:46:29 prefetch.2.10.7: 1) 'SRR2722814' was downloaded successfully Read 14720643 spots for SRR2722814/SRR2722814.sra Written 14720643 spots for SRR2722814/SRR2722814.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: 00:13:10 14720643 reads; of these: 14720643 (100.00%) were paired; of these: 745936 (5.07%) aligned concordantly 0 times 11867446 (80.62%) aligned concordantly exactly 1 time 2107261 (14.32%) aligned concordantly >1 times ---- 745936 pairs aligned concordantly 0 times; of these: 353637 (47.41%) aligned discordantly 1 time ---- 392299 pairs aligned 0 times concordantly or discordantly; of these: 784598 mates make up the pairs; of these: 409864 (52.24%) aligned 0 times 214674 (27.36%) aligned exactly 1 time 160060 (20.40%) aligned >1 times 98.61% overall alignment rate Time searching: 00:13:10 Overall time: 00:13:10 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] 183423 / 14181476 = 0.0129 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 @ Fri, 26 Jun 2020 23:09:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.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 @ Fri, 26 Jun 2020 23:09:35: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:09:35: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:09:41: 1000000 INFO @ Fri, 26 Jun 2020 23:09:46: 2000000 INFO @ Fri, 26 Jun 2020 23:09:52: 3000000 INFO @ Fri, 26 Jun 2020 23:09:57: 4000000 INFO @ Fri, 26 Jun 2020 23:10:03: 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 @ Fri, 26 Jun 2020 23:10:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.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 @ Fri, 26 Jun 2020 23:10:05: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:10:05: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:10:09: 6000000 INFO @ Fri, 26 Jun 2020 23:10:12: 1000000 INFO @ Fri, 26 Jun 2020 23:10:15: 7000000 INFO @ Fri, 26 Jun 2020 23:10:19: 2000000 INFO @ Fri, 26 Jun 2020 23:10:22: 8000000 INFO @ Fri, 26 Jun 2020 23:10:25: 3000000 INFO @ Fri, 26 Jun 2020 23:10:28: 9000000 INFO @ Fri, 26 Jun 2020 23:10:31: 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 @ Fri, 26 Jun 2020 23:10:35: 10000000 INFO @ Fri, 26 Jun 2020 23:10:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.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 @ Fri, 26 Jun 2020 23:10:35: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:10:35: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:10:38: 5000000 INFO @ Fri, 26 Jun 2020 23:10:42: 11000000 INFO @ Fri, 26 Jun 2020 23:10:43: 1000000 INFO @ Fri, 26 Jun 2020 23:10:45: 6000000 INFO @ Fri, 26 Jun 2020 23:10:49: 12000000 INFO @ Fri, 26 Jun 2020 23:10:50: 2000000 INFO @ Fri, 26 Jun 2020 23:10:52: 7000000 INFO @ Fri, 26 Jun 2020 23:10:56: 13000000 INFO @ Fri, 26 Jun 2020 23:10:58: 3000000 INFO @ Fri, 26 Jun 2020 23:10:59: 8000000 INFO @ Fri, 26 Jun 2020 23:11:02: 14000000 INFO @ Fri, 26 Jun 2020 23:11:05: 4000000 INFO @ Fri, 26 Jun 2020 23:11:06: 9000000 INFO @ Fri, 26 Jun 2020 23:11:09: 15000000 INFO @ Fri, 26 Jun 2020 23:11:13: 5000000 INFO @ Fri, 26 Jun 2020 23:11:13: 10000000 INFO @ Fri, 26 Jun 2020 23:11:16: 16000000 INFO @ Fri, 26 Jun 2020 23:11:20: 11000000 INFO @ Fri, 26 Jun 2020 23:11:20: 6000000 INFO @ Fri, 26 Jun 2020 23:11:23: 17000000 INFO @ Fri, 26 Jun 2020 23:11:27: 12000000 INFO @ Fri, 26 Jun 2020 23:11:28: 7000000 INFO @ Fri, 26 Jun 2020 23:11:30: 18000000 INFO @ Fri, 26 Jun 2020 23:11:34: 13000000 INFO @ Fri, 26 Jun 2020 23:11:35: 8000000 INFO @ Fri, 26 Jun 2020 23:11:37: 19000000 INFO @ Fri, 26 Jun 2020 23:11:41: 14000000 INFO @ Fri, 26 Jun 2020 23:11:43: 9000000 INFO @ Fri, 26 Jun 2020 23:11:44: 20000000 INFO @ Fri, 26 Jun 2020 23:11:48: 15000000 INFO @ Fri, 26 Jun 2020 23:11:51: 21000000 INFO @ Fri, 26 Jun 2020 23:11:51: 10000000 INFO @ Fri, 26 Jun 2020 23:11:55: 16000000 INFO @ Fri, 26 Jun 2020 23:11:58: 22000000 INFO @ Fri, 26 Jun 2020 23:11:59: 11000000 INFO @ Fri, 26 Jun 2020 23:12:02: 17000000 INFO @ Fri, 26 Jun 2020 23:12:05: 23000000 INFO @ Fri, 26 Jun 2020 23:12:07: 12000000 INFO @ Fri, 26 Jun 2020 23:12:09: 18000000 INFO @ Fri, 26 Jun 2020 23:12:12: 24000000 INFO @ Fri, 26 Jun 2020 23:12:15: 13000000 INFO @ Fri, 26 Jun 2020 23:12:16: 19000000 INFO @ Fri, 26 Jun 2020 23:12:19: 25000000 INFO @ Fri, 26 Jun 2020 23:12:23: 14000000 INFO @ Fri, 26 Jun 2020 23:12:23: 20000000 INFO @ Fri, 26 Jun 2020 23:12:26: 26000000 INFO @ Fri, 26 Jun 2020 23:12:30: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:12:31: 15000000 INFO @ Fri, 26 Jun 2020 23:12:33: 27000000 INFO @ Fri, 26 Jun 2020 23:12:37: 22000000 INFO @ Fri, 26 Jun 2020 23:12:38: 16000000 INFO @ Fri, 26 Jun 2020 23:12:40: 28000000 INFO @ Fri, 26 Jun 2020 23:12:44: 23000000 INFO @ Fri, 26 Jun 2020 23:12:45: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:12:45: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:12:45: #1 total tags in treatment: 13792252 INFO @ Fri, 26 Jun 2020 23:12:45: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:12:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:12:45: #1 tags after filtering in treatment: 12667796 INFO @ Fri, 26 Jun 2020 23:12:45: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 23:12:45: #1 finished! INFO @ Fri, 26 Jun 2020 23:12:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:12:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:12:46: #2 number of paired peaks: 331 WARNING @ Fri, 26 Jun 2020 23:12:46: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Fri, 26 Jun 2020 23:12:46: start model_add_line... INFO @ Fri, 26 Jun 2020 23:12:46: start X-correlation... INFO @ Fri, 26 Jun 2020 23:12:46: end of X-cor INFO @ Fri, 26 Jun 2020 23:12:46: #2 finished! INFO @ Fri, 26 Jun 2020 23:12:46: #2 predicted fragment length is 139 bps INFO @ Fri, 26 Jun 2020 23:12:46: #2 alternative fragment length(s) may be 4,139 bps INFO @ Fri, 26 Jun 2020 23:12:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.05_model.r INFO @ Fri, 26 Jun 2020 23:12:46: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:12:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:12:46: 17000000 INFO @ Fri, 26 Jun 2020 23:12:51: 24000000 INFO @ Fri, 26 Jun 2020 23:12:54: 18000000 INFO @ Fri, 26 Jun 2020 23:12:57: 25000000 INFO @ Fri, 26 Jun 2020 23:13:02: 19000000 INFO @ Fri, 26 Jun 2020 23:13:04: 26000000 INFO @ Fri, 26 Jun 2020 23:13:10: 20000000 INFO @ Fri, 26 Jun 2020 23:13:11: 27000000 INFO @ Fri, 26 Jun 2020 23:13:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:13:17: 21000000 INFO @ Fri, 26 Jun 2020 23:13:18: 28000000 INFO @ Fri, 26 Jun 2020 23:13:22: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:13:22: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:13:22: #1 total tags in treatment: 13792252 INFO @ Fri, 26 Jun 2020 23:13:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:13:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:13:22: #1 tags after filtering in treatment: 12667796 INFO @ Fri, 26 Jun 2020 23:13:22: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 23:13:22: #1 finished! INFO @ Fri, 26 Jun 2020 23:13:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:13:22: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:13:23: #2 number of paired peaks: 331 WARNING @ Fri, 26 Jun 2020 23:13:23: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Fri, 26 Jun 2020 23:13:23: start model_add_line... INFO @ Fri, 26 Jun 2020 23:13:23: start X-correlation... INFO @ Fri, 26 Jun 2020 23:13:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:13:23: end of X-cor INFO @ Fri, 26 Jun 2020 23:13:23: #2 finished! INFO @ Fri, 26 Jun 2020 23:13:23: #2 predicted fragment length is 139 bps INFO @ Fri, 26 Jun 2020 23:13:23: #2 alternative fragment length(s) may be 4,139 bps INFO @ Fri, 26 Jun 2020 23:13:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.10_model.r INFO @ Fri, 26 Jun 2020 23:13:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:13:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:13:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:13:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.05_summits.bed INFO @ Fri, 26 Jun 2020 23:13:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (574 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:13:25: 22000000 INFO @ Fri, 26 Jun 2020 23:13:32: 23000000 INFO @ Fri, 26 Jun 2020 23:13:39: 24000000 INFO @ Fri, 26 Jun 2020 23:13:46: 25000000 INFO @ Fri, 26 Jun 2020 23:13:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:13:53: 26000000 INFO @ Fri, 26 Jun 2020 23:13:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:13:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:13:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.10_summits.bed INFO @ Fri, 26 Jun 2020 23:13:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (311 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:14:00: 27000000 INFO @ Fri, 26 Jun 2020 23:14:07: 28000000 INFO @ Fri, 26 Jun 2020 23:14:12: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:14:12: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:14:12: #1 total tags in treatment: 13792252 INFO @ Fri, 26 Jun 2020 23:14:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:14:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:14:12: #1 tags after filtering in treatment: 12667796 INFO @ Fri, 26 Jun 2020 23:14:12: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 23:14:12: #1 finished! INFO @ Fri, 26 Jun 2020 23:14:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:14:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:14:13: #2 number of paired peaks: 331 WARNING @ Fri, 26 Jun 2020 23:14:13: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Fri, 26 Jun 2020 23:14:13: start model_add_line... INFO @ Fri, 26 Jun 2020 23:14:13: start X-correlation... INFO @ Fri, 26 Jun 2020 23:14:13: end of X-cor INFO @ Fri, 26 Jun 2020 23:14:13: #2 finished! INFO @ Fri, 26 Jun 2020 23:14:13: #2 predicted fragment length is 139 bps INFO @ Fri, 26 Jun 2020 23:14:13: #2 alternative fragment length(s) may be 4,139 bps INFO @ Fri, 26 Jun 2020 23:14:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.20_model.r INFO @ Fri, 26 Jun 2020 23:14:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:14:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:14:38: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:14:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:14:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:14:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353660/SRX1353660.20_summits.bed INFO @ Fri, 26 Jun 2020 23:14:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (204 records, 4 fields): 3 millis CompletedMACS2peakCalling