Job ID = 6497335 SRX = SRX1353661 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:24:00 prefetch.2.10.7: 1) Downloading 'SRR2722815'... 2020-06-25T22:24:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:26:36 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:26:36 prefetch.2.10.7: 1) 'SRR2722815' was downloaded successfully Read 14588659 spots for SRR2722815/SRR2722815.sra Written 14588659 spots for SRR2722815/SRR2722815.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: 00:13:19 14588659 reads; of these: 14588659 (100.00%) were paired; of these: 531739 (3.64%) aligned concordantly 0 times 11969427 (82.05%) aligned concordantly exactly 1 time 2087493 (14.31%) aligned concordantly >1 times ---- 531739 pairs aligned concordantly 0 times; of these: 271482 (51.06%) aligned discordantly 1 time ---- 260257 pairs aligned 0 times concordantly or discordantly; of these: 520514 mates make up the pairs; of these: 238206 (45.76%) aligned 0 times 157691 (30.30%) aligned exactly 1 time 124617 (23.94%) aligned >1 times 99.18% overall alignment rate Time searching: 00:13:19 Overall time: 00:13:19 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] 204240 / 14207551 = 0.0144 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 07:49:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.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 07:49:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:49:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:50:03: 1000000 INFO @ Fri, 26 Jun 2020 07:50:08: 2000000 INFO @ Fri, 26 Jun 2020 07:50:12: 3000000 INFO @ Fri, 26 Jun 2020 07:50:17: 4000000 INFO @ Fri, 26 Jun 2020 07:50:22: 5000000 INFO @ Fri, 26 Jun 2020 07:50:26: 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 @ Fri, 26 Jun 2020 07:50:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.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 07:50:28: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:50:28: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:50:31: 7000000 INFO @ Fri, 26 Jun 2020 07:50:33: 1000000 INFO @ Fri, 26 Jun 2020 07:50:36: 8000000 INFO @ Fri, 26 Jun 2020 07:50:38: 2000000 INFO @ Fri, 26 Jun 2020 07:50:41: 9000000 INFO @ Fri, 26 Jun 2020 07:50:43: 3000000 INFO @ Fri, 26 Jun 2020 07:50:46: 10000000 INFO @ Fri, 26 Jun 2020 07:50:48: 4000000 INFO @ Fri, 26 Jun 2020 07:50:51: 11000000 INFO @ Fri, 26 Jun 2020 07:50:53: 5000000 INFO @ Fri, 26 Jun 2020 07:50:56: 12000000 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 07:50:58: 6000000 INFO @ Fri, 26 Jun 2020 07:50:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.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 07:50:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:50:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:51:01: 13000000 INFO @ Fri, 26 Jun 2020 07:51:03: 7000000 INFO @ Fri, 26 Jun 2020 07:51:03: 1000000 INFO @ Fri, 26 Jun 2020 07:51:06: 14000000 INFO @ Fri, 26 Jun 2020 07:51:08: 8000000 INFO @ Fri, 26 Jun 2020 07:51:09: 2000000 INFO @ Fri, 26 Jun 2020 07:51:10: 15000000 INFO @ Fri, 26 Jun 2020 07:51:13: 9000000 INFO @ Fri, 26 Jun 2020 07:51:14: 3000000 INFO @ Fri, 26 Jun 2020 07:51:15: 16000000 INFO @ Fri, 26 Jun 2020 07:51:18: 10000000 INFO @ Fri, 26 Jun 2020 07:51:19: 4000000 INFO @ Fri, 26 Jun 2020 07:51:20: 17000000 INFO @ Fri, 26 Jun 2020 07:51:23: 11000000 INFO @ Fri, 26 Jun 2020 07:51:23: 5000000 INFO @ Fri, 26 Jun 2020 07:51:25: 18000000 INFO @ Fri, 26 Jun 2020 07:51:28: 12000000 INFO @ Fri, 26 Jun 2020 07:51:28: 6000000 INFO @ Fri, 26 Jun 2020 07:51:30: 19000000 INFO @ Fri, 26 Jun 2020 07:51:33: 13000000 INFO @ Fri, 26 Jun 2020 07:51:33: 7000000 INFO @ Fri, 26 Jun 2020 07:51:35: 20000000 INFO @ Fri, 26 Jun 2020 07:51:37: 14000000 INFO @ Fri, 26 Jun 2020 07:51:38: 8000000 INFO @ Fri, 26 Jun 2020 07:51:40: 21000000 INFO @ Fri, 26 Jun 2020 07:51:42: 15000000 INFO @ Fri, 26 Jun 2020 07:51:43: 9000000 INFO @ Fri, 26 Jun 2020 07:51:45: 22000000 INFO @ Fri, 26 Jun 2020 07:51:47: 16000000 INFO @ Fri, 26 Jun 2020 07:51:48: 10000000 INFO @ Fri, 26 Jun 2020 07:51:50: 23000000 INFO @ Fri, 26 Jun 2020 07:51:52: 17000000 INFO @ Fri, 26 Jun 2020 07:51:53: 11000000 INFO @ Fri, 26 Jun 2020 07:51:55: 24000000 INFO @ Fri, 26 Jun 2020 07:51:57: 18000000 INFO @ Fri, 26 Jun 2020 07:51:58: 12000000 INFO @ Fri, 26 Jun 2020 07:52:00: 25000000 INFO @ Fri, 26 Jun 2020 07:52:02: 19000000 INFO @ Fri, 26 Jun 2020 07:52:03: 13000000 INFO @ Fri, 26 Jun 2020 07:52:05: 26000000 INFO @ Fri, 26 Jun 2020 07:52:07: 20000000 INFO @ Fri, 26 Jun 2020 07:52:08: 14000000 INFO @ Fri, 26 Jun 2020 07:52:09: 27000000 INFO @ Fri, 26 Jun 2020 07:52:12: 21000000 INFO @ Fri, 26 Jun 2020 07:52:13: 15000000 INFO @ Fri, 26 Jun 2020 07:52:14: 28000000 INFO @ Fri, 26 Jun 2020 07:52:17: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:52:17: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:52:17: #1 total tags in treatment: 13853347 INFO @ Fri, 26 Jun 2020 07:52:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:52:17: #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 07:52:17: 22000000 INFO @ Fri, 26 Jun 2020 07:52:17: #1 tags after filtering in treatment: 12714380 INFO @ Fri, 26 Jun 2020 07:52:17: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 07:52:17: #1 finished! INFO @ Fri, 26 Jun 2020 07:52:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:52:17: 16000000 INFO @ Fri, 26 Jun 2020 07:52:18: #2 number of paired peaks: 329 WARNING @ Fri, 26 Jun 2020 07:52:18: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Fri, 26 Jun 2020 07:52:18: start model_add_line... INFO @ Fri, 26 Jun 2020 07:52:18: start X-correlation... INFO @ Fri, 26 Jun 2020 07:52:18: end of X-cor INFO @ Fri, 26 Jun 2020 07:52:18: #2 finished! INFO @ Fri, 26 Jun 2020 07:52:18: #2 predicted fragment length is 140 bps INFO @ Fri, 26 Jun 2020 07:52:18: #2 alternative fragment length(s) may be 4,124,140 bps INFO @ Fri, 26 Jun 2020 07:52:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.05_model.r INFO @ Fri, 26 Jun 2020 07:52:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:52:22: 23000000 INFO @ Fri, 26 Jun 2020 07:52:22: 17000000 INFO @ Fri, 26 Jun 2020 07:52:27: 24000000 INFO @ Fri, 26 Jun 2020 07:52:27: 18000000 INFO @ Fri, 26 Jun 2020 07:52:32: 25000000 INFO @ Fri, 26 Jun 2020 07:52:32: 19000000 INFO @ Fri, 26 Jun 2020 07:52:37: 26000000 INFO @ Fri, 26 Jun 2020 07:52:37: 20000000 INFO @ Fri, 26 Jun 2020 07:52:42: 27000000 INFO @ Fri, 26 Jun 2020 07:52:42: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:52:42: 21000000 INFO @ Fri, 26 Jun 2020 07:52:46: 28000000 INFO @ Fri, 26 Jun 2020 07:52:47: 22000000 INFO @ Fri, 26 Jun 2020 07:52:49: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:52:49: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:52:49: #1 total tags in treatment: 13853347 INFO @ Fri, 26 Jun 2020 07:52:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:52:49: #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 07:52:49: #1 tags after filtering in treatment: 12714380 INFO @ Fri, 26 Jun 2020 07:52:49: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 07:52:49: #1 finished! INFO @ Fri, 26 Jun 2020 07:52:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:52:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:52:50: #2 number of paired peaks: 329 WARNING @ Fri, 26 Jun 2020 07:52:50: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Fri, 26 Jun 2020 07:52:50: start model_add_line... INFO @ Fri, 26 Jun 2020 07:52:50: start X-correlation... INFO @ Fri, 26 Jun 2020 07:52:50: end of X-cor INFO @ Fri, 26 Jun 2020 07:52:50: #2 finished! INFO @ Fri, 26 Jun 2020 07:52:50: #2 predicted fragment length is 140 bps INFO @ Fri, 26 Jun 2020 07:52:50: #2 alternative fragment length(s) may be 4,124,140 bps INFO @ Fri, 26 Jun 2020 07:52:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.10_model.r INFO @ Fri, 26 Jun 2020 07:52:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:52:50: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:52:52: 23000000 INFO @ Fri, 26 Jun 2020 07:52:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:52:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:52:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.05_summits.bed INFO @ Fri, 26 Jun 2020 07:52:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (792 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:52:56: 24000000 INFO @ Fri, 26 Jun 2020 07:53:01: 25000000 INFO @ Fri, 26 Jun 2020 07:53:05: 26000000 INFO @ Fri, 26 Jun 2020 07:53:10: 27000000 INFO @ Fri, 26 Jun 2020 07:53:15: 28000000 INFO @ Fri, 26 Jun 2020 07:53:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:53:17: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:53:17: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:53:17: #1 total tags in treatment: 13853347 INFO @ Fri, 26 Jun 2020 07:53:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:53:17: #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 07:53:17: #1 tags after filtering in treatment: 12714380 INFO @ Fri, 26 Jun 2020 07:53:17: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 07:53:17: #1 finished! INFO @ Fri, 26 Jun 2020 07:53:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:53:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:53:18: #2 number of paired peaks: 329 WARNING @ Fri, 26 Jun 2020 07:53:18: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Fri, 26 Jun 2020 07:53:18: start model_add_line... INFO @ Fri, 26 Jun 2020 07:53:18: start X-correlation... INFO @ Fri, 26 Jun 2020 07:53:18: end of X-cor INFO @ Fri, 26 Jun 2020 07:53:18: #2 finished! INFO @ Fri, 26 Jun 2020 07:53:18: #2 predicted fragment length is 140 bps INFO @ Fri, 26 Jun 2020 07:53:18: #2 alternative fragment length(s) may be 4,124,140 bps INFO @ Fri, 26 Jun 2020 07:53:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.20_model.r INFO @ Fri, 26 Jun 2020 07:53:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:53:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:53:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:53:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:53:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.10_summits.bed INFO @ Fri, 26 Jun 2020 07:53:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (308 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:53:44: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:53:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:53:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:53:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353661/SRX1353661.20_summits.bed INFO @ Fri, 26 Jun 2020 07:53:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (203 records, 4 fields): 56 millis CompletedMACS2peakCalling