Job ID = 6366920 SRX = SRX2576623 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:06:38 prefetch.2.10.7: 1) Downloading 'SRR5272580'... 2020-06-15T23:06:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:08:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:08:25 prefetch.2.10.7: 1) 'SRR5272580' was downloaded successfully Read 21385259 spots for SRR5272580/SRR5272580.sra Written 21385259 spots for SRR5272580/SRR5272580.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: 00:04:57 21385259 reads; of these: 21385259 (100.00%) were unpaired; of these: 1041765 (4.87%) aligned 0 times 16660937 (77.91%) aligned exactly 1 time 3682557 (17.22%) aligned >1 times 95.13% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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_rmdupse_core] 6046589 / 20343494 = 0.2972 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 08:19:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.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 08:19:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:23: 1000000 INFO @ Tue, 16 Jun 2020 08:19:30: 2000000 INFO @ Tue, 16 Jun 2020 08:19:37: 3000000 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 08:19:45: 4000000 INFO @ Tue, 16 Jun 2020 08:19:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.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 08:19:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:53: 5000000 INFO @ Tue, 16 Jun 2020 08:19:54: 1000000 INFO @ Tue, 16 Jun 2020 08:20:01: 6000000 INFO @ Tue, 16 Jun 2020 08:20:02: 2000000 INFO @ Tue, 16 Jun 2020 08:20:09: 7000000 INFO @ Tue, 16 Jun 2020 08:20:10: 3000000 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 08:20:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.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 08:20:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:18: 8000000 INFO @ Tue, 16 Jun 2020 08:20:19: 4000000 INFO @ Tue, 16 Jun 2020 08:20:24: 1000000 INFO @ Tue, 16 Jun 2020 08:20:26: 9000000 INFO @ Tue, 16 Jun 2020 08:20:27: 5000000 INFO @ Tue, 16 Jun 2020 08:20:32: 2000000 INFO @ Tue, 16 Jun 2020 08:20:35: 10000000 INFO @ Tue, 16 Jun 2020 08:20:35: 6000000 INFO @ Tue, 16 Jun 2020 08:20:40: 3000000 INFO @ Tue, 16 Jun 2020 08:20:43: 11000000 INFO @ Tue, 16 Jun 2020 08:20:44: 7000000 INFO @ Tue, 16 Jun 2020 08:20:49: 4000000 INFO @ Tue, 16 Jun 2020 08:20:51: 12000000 INFO @ Tue, 16 Jun 2020 08:20:52: 8000000 INFO @ Tue, 16 Jun 2020 08:20:57: 5000000 INFO @ Tue, 16 Jun 2020 08:20:59: 13000000 INFO @ Tue, 16 Jun 2020 08:21:00: 9000000 INFO @ Tue, 16 Jun 2020 08:21:05: 6000000 INFO @ Tue, 16 Jun 2020 08:21:07: 14000000 INFO @ Tue, 16 Jun 2020 08:21:08: 10000000 INFO @ Tue, 16 Jun 2020 08:21:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:21:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:21:10: #1 total tags in treatment: 14296905 INFO @ Tue, 16 Jun 2020 08:21:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:10: #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 08:21:10: #1 tags after filtering in treatment: 14296905 INFO @ Tue, 16 Jun 2020 08:21:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:11: #2 number of paired peaks: 439 WARNING @ Tue, 16 Jun 2020 08:21:11: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:11: #2 predicted fragment length is 150 bps INFO @ Tue, 16 Jun 2020 08:21:11: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 16 Jun 2020 08:21:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.05_model.r INFO @ Tue, 16 Jun 2020 08:21:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:14: 7000000 INFO @ Tue, 16 Jun 2020 08:21:17: 11000000 INFO @ Tue, 16 Jun 2020 08:21:22: 8000000 INFO @ Tue, 16 Jun 2020 08:21:25: 12000000 INFO @ Tue, 16 Jun 2020 08:21:30: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:21:33: 13000000 INFO @ Tue, 16 Jun 2020 08:21:38: 10000000 INFO @ Tue, 16 Jun 2020 08:21:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:41: 14000000 INFO @ Tue, 16 Jun 2020 08:21:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:21:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:21:44: #1 total tags in treatment: 14296905 INFO @ Tue, 16 Jun 2020 08:21:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:44: #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 08:21:44: #1 tags after filtering in treatment: 14296905 INFO @ Tue, 16 Jun 2020 08:21:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:45: #2 number of paired peaks: 439 WARNING @ Tue, 16 Jun 2020 08:21:45: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:45: #2 predicted fragment length is 150 bps INFO @ Tue, 16 Jun 2020 08:21:45: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 16 Jun 2020 08:21:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.10_model.r INFO @ Tue, 16 Jun 2020 08:21:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:46: 11000000 INFO @ Tue, 16 Jun 2020 08:21:54: 12000000 INFO @ Tue, 16 Jun 2020 08:21:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.05_summits.bed INFO @ Tue, 16 Jun 2020 08:21:55: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1821 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:22:01: 13000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:22:09: 14000000 INFO @ Tue, 16 Jun 2020 08:22:11: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:22:11: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:22:11: #1 total tags in treatment: 14296905 INFO @ Tue, 16 Jun 2020 08:22:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:11: #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 08:22:11: #1 tags after filtering in treatment: 14296905 INFO @ Tue, 16 Jun 2020 08:22:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:11: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:12: #2 number of paired peaks: 439 WARNING @ Tue, 16 Jun 2020 08:22:12: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:12: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:12: #2 predicted fragment length is 150 bps INFO @ Tue, 16 Jun 2020 08:22:12: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 16 Jun 2020 08:22:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.20_model.r INFO @ Tue, 16 Jun 2020 08:22:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.10_summits.bed INFO @ Tue, 16 Jun 2020 08:22:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1344 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:22:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576623/SRX2576623.20_summits.bed INFO @ Tue, 16 Jun 2020 08:22:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (910 records, 4 fields): 6 millis CompletedMACS2peakCalling