Job ID = 6367628 SRX = SRX3583340 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:30:35 prefetch.2.10.7: 1) Downloading 'SRR6493996'... 2020-06-15T23:30:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:36:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:36:11 prefetch.2.10.7: 1) 'SRR6493996' was downloaded successfully 2020-06-15T23:36:11 prefetch.2.10.7: 'SRR6493996' has 0 unresolved dependencies Read 33757140 spots for SRR6493996/SRR6493996.sra Written 33757140 spots for SRR6493996/SRR6493996.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: 00:10:55 33757140 reads; of these: 33757140 (100.00%) were unpaired; of these: 756982 (2.24%) aligned 0 times 28926580 (85.69%) aligned exactly 1 time 4073578 (12.07%) aligned >1 times 97.76% overall alignment rate Time searching: 00:10:55 Overall time: 00:10:55 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_rmdupse_core] 6677286 / 33000158 = 0.2023 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 08:57:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.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 08:57:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:57:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:57:51: 1000000 INFO @ Tue, 16 Jun 2020 08:57:58: 2000000 INFO @ Tue, 16 Jun 2020 08:58:04: 3000000 INFO @ Tue, 16 Jun 2020 08:58:11: 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 @ Tue, 16 Jun 2020 08:58:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.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 08:58:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:18: 5000000 INFO @ Tue, 16 Jun 2020 08:58:22: 1000000 INFO @ Tue, 16 Jun 2020 08:58:26: 6000000 INFO @ Tue, 16 Jun 2020 08:58:30: 2000000 INFO @ Tue, 16 Jun 2020 08:58:33: 7000000 INFO @ Tue, 16 Jun 2020 08:58:37: 3000000 INFO @ Tue, 16 Jun 2020 08:58:41: 8000000 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 08:58:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.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 08:58:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:45: 4000000 INFO @ Tue, 16 Jun 2020 08:58:48: 9000000 INFO @ Tue, 16 Jun 2020 08:58:52: 1000000 INFO @ Tue, 16 Jun 2020 08:58:53: 5000000 INFO @ Tue, 16 Jun 2020 08:58:56: 10000000 INFO @ Tue, 16 Jun 2020 08:59:00: 2000000 INFO @ Tue, 16 Jun 2020 08:59:01: 6000000 INFO @ Tue, 16 Jun 2020 08:59:03: 11000000 INFO @ Tue, 16 Jun 2020 08:59:08: 3000000 INFO @ Tue, 16 Jun 2020 08:59:08: 7000000 INFO @ Tue, 16 Jun 2020 08:59:11: 12000000 INFO @ Tue, 16 Jun 2020 08:59:16: 4000000 INFO @ Tue, 16 Jun 2020 08:59:16: 8000000 INFO @ Tue, 16 Jun 2020 08:59:18: 13000000 INFO @ Tue, 16 Jun 2020 08:59:24: 5000000 INFO @ Tue, 16 Jun 2020 08:59:24: 9000000 INFO @ Tue, 16 Jun 2020 08:59:26: 14000000 INFO @ Tue, 16 Jun 2020 08:59:31: 6000000 INFO @ Tue, 16 Jun 2020 08:59:31: 10000000 INFO @ Tue, 16 Jun 2020 08:59:34: 15000000 INFO @ Tue, 16 Jun 2020 08:59:39: 7000000 INFO @ Tue, 16 Jun 2020 08:59:39: 11000000 INFO @ Tue, 16 Jun 2020 08:59:42: 16000000 INFO @ Tue, 16 Jun 2020 08:59:47: 12000000 INFO @ Tue, 16 Jun 2020 08:59:47: 8000000 INFO @ Tue, 16 Jun 2020 08:59:50: 17000000 INFO @ Tue, 16 Jun 2020 08:59:54: 13000000 INFO @ Tue, 16 Jun 2020 08:59:55: 9000000 INFO @ Tue, 16 Jun 2020 08:59:57: 18000000 INFO @ Tue, 16 Jun 2020 09:00:02: 14000000 INFO @ Tue, 16 Jun 2020 09:00:02: 10000000 INFO @ Tue, 16 Jun 2020 09:00:05: 19000000 INFO @ Tue, 16 Jun 2020 09:00:10: 15000000 INFO @ Tue, 16 Jun 2020 09:00:10: 11000000 INFO @ Tue, 16 Jun 2020 09:00:13: 20000000 INFO @ Tue, 16 Jun 2020 09:00:18: 16000000 INFO @ Tue, 16 Jun 2020 09:00:18: 12000000 INFO @ Tue, 16 Jun 2020 09:00:21: 21000000 INFO @ Tue, 16 Jun 2020 09:00:26: 17000000 INFO @ Tue, 16 Jun 2020 09:00:26: 13000000 INFO @ Tue, 16 Jun 2020 09:00:29: 22000000 INFO @ Tue, 16 Jun 2020 09:00:34: 14000000 INFO @ Tue, 16 Jun 2020 09:00:34: 18000000 INFO @ Tue, 16 Jun 2020 09:00:37: 23000000 INFO @ Tue, 16 Jun 2020 09:00:42: 19000000 INFO @ Tue, 16 Jun 2020 09:00:42: 15000000 INFO @ Tue, 16 Jun 2020 09:00:45: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:00:50: 20000000 INFO @ Tue, 16 Jun 2020 09:00:50: 16000000 INFO @ Tue, 16 Jun 2020 09:00:53: 25000000 INFO @ Tue, 16 Jun 2020 09:00:57: 21000000 INFO @ Tue, 16 Jun 2020 09:00:58: 17000000 INFO @ Tue, 16 Jun 2020 09:01:01: 26000000 INFO @ Tue, 16 Jun 2020 09:01:04: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:01:04: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:01:04: #1 total tags in treatment: 26322872 INFO @ Tue, 16 Jun 2020 09:01:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:04: #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 09:01:04: #1 tags after filtering in treatment: 26322872 INFO @ Tue, 16 Jun 2020 09:01:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:01:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:05: 22000000 INFO @ Tue, 16 Jun 2020 09:01:06: 18000000 INFO @ Tue, 16 Jun 2020 09:01:06: #2 number of paired peaks: 592 WARNING @ Tue, 16 Jun 2020 09:01:06: Fewer paired peaks (592) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 592 pairs to build model! INFO @ Tue, 16 Jun 2020 09:01:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:07: #2 predicted fragment length is 168 bps INFO @ Tue, 16 Jun 2020 09:01:07: #2 alternative fragment length(s) may be 3,168 bps INFO @ Tue, 16 Jun 2020 09:01:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.05_model.r INFO @ Tue, 16 Jun 2020 09:01:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:13: 23000000 INFO @ Tue, 16 Jun 2020 09:01:14: 19000000 INFO @ Tue, 16 Jun 2020 09:01:21: 24000000 INFO @ Tue, 16 Jun 2020 09:01:22: 20000000 INFO @ Tue, 16 Jun 2020 09:01:29: 25000000 INFO @ Tue, 16 Jun 2020 09:01:30: 21000000 INFO @ Tue, 16 Jun 2020 09:01:37: 26000000 INFO @ Tue, 16 Jun 2020 09:01:38: 22000000 INFO @ Tue, 16 Jun 2020 09:01:39: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:01:39: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:01:39: #1 total tags in treatment: 26322872 INFO @ Tue, 16 Jun 2020 09:01:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:39: #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 09:01:40: #1 tags after filtering in treatment: 26322872 INFO @ Tue, 16 Jun 2020 09:01:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:01:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:42: #2 number of paired peaks: 592 WARNING @ Tue, 16 Jun 2020 09:01:42: Fewer paired peaks (592) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 592 pairs to build model! INFO @ Tue, 16 Jun 2020 09:01:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:42: #2 predicted fragment length is 168 bps INFO @ Tue, 16 Jun 2020 09:01:42: #2 alternative fragment length(s) may be 3,168 bps INFO @ Tue, 16 Jun 2020 09:01:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.10_model.r INFO @ Tue, 16 Jun 2020 09:01:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:45: 23000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:01:53: 24000000 INFO @ Tue, 16 Jun 2020 09:02:00: 25000000 INFO @ Tue, 16 Jun 2020 09:02:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:07: 26000000 INFO @ Tue, 16 Jun 2020 09:02:10: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:02:10: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:02:10: #1 total tags in treatment: 26322872 INFO @ Tue, 16 Jun 2020 09:02:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:10: #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 09:02:10: #1 tags after filtering in treatment: 26322872 INFO @ Tue, 16 Jun 2020 09:02:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:02:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:12: #2 number of paired peaks: 592 WARNING @ Tue, 16 Jun 2020 09:02:12: Fewer paired peaks (592) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 592 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:13: #2 predicted fragment length is 168 bps INFO @ Tue, 16 Jun 2020 09:02:13: #2 alternative fragment length(s) may be 3,168 bps INFO @ Tue, 16 Jun 2020 09:02:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.20_model.r INFO @ Tue, 16 Jun 2020 09:02:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.05_summits.bed INFO @ Tue, 16 Jun 2020 09:02:32: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5924 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:02:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.10_summits.bed INFO @ Tue, 16 Jun 2020 09:03:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4435 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:03:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3583340/SRX3583340.20_summits.bed INFO @ Tue, 16 Jun 2020 09:03:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3287 records, 4 fields): 26 millis CompletedMACS2peakCalling