Job ID = 6507722 SRX = SRX1353661 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:08:21 prefetch.2.10.7: 1) Downloading 'SRR2722815'... 2020-06-26T13:08:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:09:57 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:09:57 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:42 14588659 reads; of these: 14588659 (100.00%) were paired; of these: 531650 (3.64%) aligned concordantly 0 times 11969400 (82.05%) aligned concordantly exactly 1 time 2087609 (14.31%) aligned concordantly >1 times ---- 531650 pairs aligned concordantly 0 times; of these: 271506 (51.07%) aligned discordantly 1 time ---- 260144 pairs aligned 0 times concordantly or discordantly; of these: 520288 mates make up the pairs; of these: 238020 (45.75%) aligned 0 times 157666 (30.30%) aligned exactly 1 time 124602 (23.95%) aligned >1 times 99.18% overall alignment rate Time searching: 00:12:43 Overall time: 00:12:43 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] 204248 / 14207657 = 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 22:32:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 22:32:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:32:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:33:01: 1000000 INFO @ Fri, 26 Jun 2020 22:33:07: 2000000 INFO @ Fri, 26 Jun 2020 22:33:13: 3000000 INFO @ Fri, 26 Jun 2020 22:33:19: 4000000 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 22:33:25: 5000000 INFO @ Fri, 26 Jun 2020 22:33:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 22:33:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:33:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:33:31: 1000000 INFO @ Fri, 26 Jun 2020 22:33:31: 6000000 INFO @ Fri, 26 Jun 2020 22:33:37: 2000000 INFO @ Fri, 26 Jun 2020 22:33:38: 7000000 INFO @ Fri, 26 Jun 2020 22:33:42: 3000000 INFO @ Fri, 26 Jun 2020 22:33:44: 8000000 INFO @ Fri, 26 Jun 2020 22:33:48: 4000000 INFO @ Fri, 26 Jun 2020 22:33:50: 9000000 INFO @ Fri, 26 Jun 2020 22:33:53: 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 @ Fri, 26 Jun 2020 22:33:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 22:33:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:33:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:33:57: 10000000 INFO @ Fri, 26 Jun 2020 22:33:59: 6000000 INFO @ Fri, 26 Jun 2020 22:34:02: 1000000 INFO @ Fri, 26 Jun 2020 22:34:03: 11000000 INFO @ Fri, 26 Jun 2020 22:34:04: 7000000 INFO @ Fri, 26 Jun 2020 22:34:07: 2000000 INFO @ Fri, 26 Jun 2020 22:34:09: 12000000 INFO @ Fri, 26 Jun 2020 22:34:10: 8000000 INFO @ Fri, 26 Jun 2020 22:34:13: 3000000 INFO @ Fri, 26 Jun 2020 22:34:16: 9000000 INFO @ Fri, 26 Jun 2020 22:34:16: 13000000 INFO @ Fri, 26 Jun 2020 22:34:19: 4000000 INFO @ Fri, 26 Jun 2020 22:34:21: 10000000 INFO @ Fri, 26 Jun 2020 22:34:22: 14000000 INFO @ Fri, 26 Jun 2020 22:34:25: 5000000 INFO @ Fri, 26 Jun 2020 22:34:27: 11000000 INFO @ Fri, 26 Jun 2020 22:34:29: 15000000 INFO @ Fri, 26 Jun 2020 22:34:30: 6000000 INFO @ Fri, 26 Jun 2020 22:34:33: 12000000 INFO @ Fri, 26 Jun 2020 22:34:35: 16000000 INFO @ Fri, 26 Jun 2020 22:34:36: 7000000 INFO @ Fri, 26 Jun 2020 22:34:39: 13000000 INFO @ Fri, 26 Jun 2020 22:34:42: 17000000 INFO @ Fri, 26 Jun 2020 22:34:42: 8000000 INFO @ Fri, 26 Jun 2020 22:34:44: 14000000 INFO @ Fri, 26 Jun 2020 22:34:48: 9000000 INFO @ Fri, 26 Jun 2020 22:34:49: 18000000 INFO @ Fri, 26 Jun 2020 22:34:50: 15000000 INFO @ Fri, 26 Jun 2020 22:34:54: 10000000 INFO @ Fri, 26 Jun 2020 22:34:55: 19000000 INFO @ Fri, 26 Jun 2020 22:34:56: 16000000 INFO @ Fri, 26 Jun 2020 22:35:00: 11000000 INFO @ Fri, 26 Jun 2020 22:35:01: 17000000 INFO @ Fri, 26 Jun 2020 22:35:02: 20000000 INFO @ Fri, 26 Jun 2020 22:35:05: 12000000 INFO @ Fri, 26 Jun 2020 22:35:07: 18000000 INFO @ Fri, 26 Jun 2020 22:35:09: 21000000 INFO @ Fri, 26 Jun 2020 22:35:11: 13000000 INFO @ Fri, 26 Jun 2020 22:35:13: 19000000 INFO @ Fri, 26 Jun 2020 22:35:15: 22000000 INFO @ Fri, 26 Jun 2020 22:35:17: 14000000 INFO @ Fri, 26 Jun 2020 22:35:19: 20000000 INFO @ Fri, 26 Jun 2020 22:35:22: 23000000 INFO @ Fri, 26 Jun 2020 22:35:23: 15000000 INFO @ Fri, 26 Jun 2020 22:35:25: 21000000 INFO @ Fri, 26 Jun 2020 22:35:29: 24000000 INFO @ Fri, 26 Jun 2020 22:35:29: 16000000 INFO @ Fri, 26 Jun 2020 22:35:30: 22000000 INFO @ Fri, 26 Jun 2020 22:35:35: 17000000 INFO @ Fri, 26 Jun 2020 22:35:36: 25000000 INFO @ Fri, 26 Jun 2020 22:35:36: 23000000 INFO @ Fri, 26 Jun 2020 22:35:41: 18000000 INFO @ Fri, 26 Jun 2020 22:35:42: 24000000 INFO @ Fri, 26 Jun 2020 22:35:43: 26000000 INFO @ Fri, 26 Jun 2020 22:35:47: 19000000 INFO @ Fri, 26 Jun 2020 22:35:48: 25000000 INFO @ Fri, 26 Jun 2020 22:35:49: 27000000 INFO @ Fri, 26 Jun 2020 22:35:53: 20000000 INFO @ Fri, 26 Jun 2020 22:35:54: 26000000 INFO @ Fri, 26 Jun 2020 22:35:56: 28000000 INFO @ Fri, 26 Jun 2020 22:35:59: 21000000 INFO @ Fri, 26 Jun 2020 22:35:59: 27000000 INFO @ Fri, 26 Jun 2020 22:35:59: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:35:59: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:35:59: #1 total tags in treatment: 13853428 INFO @ Fri, 26 Jun 2020 22:35:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:35:59: #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 22:36:00: #1 tags after filtering in treatment: 12714406 INFO @ Fri, 26 Jun 2020 22:36:00: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 22:36:00: #1 finished! INFO @ Fri, 26 Jun 2020 22:36:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:36:01: #2 number of paired peaks: 328 WARNING @ Fri, 26 Jun 2020 22:36:01: 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 @ Fri, 26 Jun 2020 22:36:01: start model_add_line... INFO @ Fri, 26 Jun 2020 22:36:01: start X-correlation... INFO @ Fri, 26 Jun 2020 22:36:01: end of X-cor INFO @ Fri, 26 Jun 2020 22:36:01: #2 finished! INFO @ Fri, 26 Jun 2020 22:36:01: #2 predicted fragment length is 140 bps INFO @ Fri, 26 Jun 2020 22:36:01: #2 alternative fragment length(s) may be 4,125,140 bps INFO @ Fri, 26 Jun 2020 22:36:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.05_model.r INFO @ Fri, 26 Jun 2020 22:36:01: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:36:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:36:05: 22000000 INFO @ Fri, 26 Jun 2020 22:36:05: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:36:08: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:36:08: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:36:08: #1 total tags in treatment: 13853428 INFO @ Fri, 26 Jun 2020 22:36:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:36:08: #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 22:36:08: #1 tags after filtering in treatment: 12714406 INFO @ Fri, 26 Jun 2020 22:36:08: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 22:36:08: #1 finished! INFO @ Fri, 26 Jun 2020 22:36:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:36:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:36:09: #2 number of paired peaks: 328 WARNING @ Fri, 26 Jun 2020 22:36:09: 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 @ Fri, 26 Jun 2020 22:36:09: start model_add_line... INFO @ Fri, 26 Jun 2020 22:36:09: start X-correlation... INFO @ Fri, 26 Jun 2020 22:36:09: end of X-cor INFO @ Fri, 26 Jun 2020 22:36:09: #2 finished! INFO @ Fri, 26 Jun 2020 22:36:09: #2 predicted fragment length is 140 bps INFO @ Fri, 26 Jun 2020 22:36:09: #2 alternative fragment length(s) may be 4,125,140 bps INFO @ Fri, 26 Jun 2020 22:36:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.10_model.r INFO @ Fri, 26 Jun 2020 22:36:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:36:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:36:10: 23000000 INFO @ Fri, 26 Jun 2020 22:36:16: 24000000 INFO @ Fri, 26 Jun 2020 22:36:21: 25000000 INFO @ Fri, 26 Jun 2020 22:36:27: 26000000 INFO @ Fri, 26 Jun 2020 22:36:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:36:32: 27000000 INFO @ Fri, 26 Jun 2020 22:36:37: 28000000 INFO @ Fri, 26 Jun 2020 22:36:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:36:40: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:36:40: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:36:40: #1 total tags in treatment: 13853428 INFO @ Fri, 26 Jun 2020 22:36:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:36:40: #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 22:36:40: #1 tags after filtering in treatment: 12714406 INFO @ Fri, 26 Jun 2020 22:36:40: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 22:36:40: #1 finished! INFO @ Fri, 26 Jun 2020 22:36:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:36:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:36:41: #2 number of paired peaks: 328 WARNING @ Fri, 26 Jun 2020 22:36:41: 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 @ Fri, 26 Jun 2020 22:36:41: start model_add_line... INFO @ Fri, 26 Jun 2020 22:36:41: start X-correlation... INFO @ Fri, 26 Jun 2020 22:36:41: end of X-cor INFO @ Fri, 26 Jun 2020 22:36:41: #2 finished! INFO @ Fri, 26 Jun 2020 22:36:41: #2 predicted fragment length is 140 bps INFO @ Fri, 26 Jun 2020 22:36:41: #2 alternative fragment length(s) may be 4,125,140 bps INFO @ Fri, 26 Jun 2020 22:36:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.20_model.r INFO @ Fri, 26 Jun 2020 22:36:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:36:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:36:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:36:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:36:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.05_summits.bed INFO @ Fri, 26 Jun 2020 22:36:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (791 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:36:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:36:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:36:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.10_summits.bed INFO @ Fri, 26 Jun 2020 22:36:51: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (309 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:37:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:37:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:37:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:37:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353661/SRX1353661.20_summits.bed INFO @ Fri, 26 Jun 2020 22:37:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (203 records, 4 fields): 2 millis CompletedMACS2peakCalling