Job ID = 6366940 SRX = SRX2576641 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:14:18 prefetch.2.10.7: 1) Downloading 'SRR5272598'... 2020-06-15T23:14:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:15:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:15:17 prefetch.2.10.7: 'SRR5272598' is valid 2020-06-15T23:15:17 prefetch.2.10.7: 1) 'SRR5272598' was downloaded successfully 2020-06-15T23:15:17 prefetch.2.10.7: 'SRR5272598' has 0 unresolved dependencies Read 21697486 spots for SRR5272598/SRR5272598.sra Written 21697486 spots for SRR5272598/SRR5272598.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:01 21697486 reads; of these: 21697486 (100.00%) were unpaired; of these: 2100320 (9.68%) aligned 0 times 16097184 (74.19%) aligned exactly 1 time 3499982 (16.13%) aligned >1 times 90.32% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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 8 files... [bam_rmdupse_core] 10157097 / 19597166 = 0.5183 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 08:25:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.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 08:25:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:17: 1000000 INFO @ Tue, 16 Jun 2020 08:25:22: 2000000 INFO @ Tue, 16 Jun 2020 08:25:27: 3000000 INFO @ Tue, 16 Jun 2020 08:25:32: 4000000 INFO @ Tue, 16 Jun 2020 08:25:37: 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 @ Tue, 16 Jun 2020 08:25:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.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 08:25:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:42: 6000000 INFO @ Tue, 16 Jun 2020 08:25:47: 1000000 INFO @ Tue, 16 Jun 2020 08:25:47: 7000000 INFO @ Tue, 16 Jun 2020 08:25:52: 2000000 INFO @ Tue, 16 Jun 2020 08:25:53: 8000000 INFO @ Tue, 16 Jun 2020 08:25:57: 3000000 INFO @ Tue, 16 Jun 2020 08:25:58: 9000000 INFO @ Tue, 16 Jun 2020 08:26:00: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:00: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:00: #1 total tags in treatment: 9440069 INFO @ Tue, 16 Jun 2020 08:26:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:00: #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 08:26:00: #1 tags after filtering in treatment: 9440069 INFO @ Tue, 16 Jun 2020 08:26:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:01: #2 number of paired peaks: 566 WARNING @ Tue, 16 Jun 2020 08:26:01: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:01: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 08:26:01: #2 alternative fragment length(s) may be 110,576 bps INFO @ Tue, 16 Jun 2020 08:26:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.05_model.r INFO @ Tue, 16 Jun 2020 08:26:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:02: 4000000 INFO @ Tue, 16 Jun 2020 08:26:07: 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 @ Tue, 16 Jun 2020 08:26:12: 6000000 INFO @ Tue, 16 Jun 2020 08:26:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.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 08:26:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:17: 7000000 INFO @ Tue, 16 Jun 2020 08:26:18: 1000000 INFO @ Tue, 16 Jun 2020 08:26:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:22: 8000000 INFO @ Tue, 16 Jun 2020 08:26:23: 2000000 INFO @ Tue, 16 Jun 2020 08:26:27: 9000000 INFO @ Tue, 16 Jun 2020 08:26:29: 3000000 INFO @ Tue, 16 Jun 2020 08:26:30: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:30: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:30: #1 total tags in treatment: 9440069 INFO @ Tue, 16 Jun 2020 08:26:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:30: #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 08:26:30: #1 tags after filtering in treatment: 9440069 INFO @ Tue, 16 Jun 2020 08:26:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:31: #2 number of paired peaks: 566 WARNING @ Tue, 16 Jun 2020 08:26:31: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:31: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 08:26:31: #2 alternative fragment length(s) may be 110,576 bps INFO @ Tue, 16 Jun 2020 08:26:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.10_model.r INFO @ Tue, 16 Jun 2020 08:26:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.05_summits.bed INFO @ Tue, 16 Jun 2020 08:26:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1556 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:35: 4000000 INFO @ Tue, 16 Jun 2020 08:26:41: 5000000 INFO @ Tue, 16 Jun 2020 08:26:47: 6000000 INFO @ Tue, 16 Jun 2020 08:26:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:52: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:26:58: 8000000 INFO @ Tue, 16 Jun 2020 08:27:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.10_summits.bed INFO @ Tue, 16 Jun 2020 08:27:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1071 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:27:03: 9000000 INFO @ Tue, 16 Jun 2020 08:27:06: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:27:06: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:27:06: #1 total tags in treatment: 9440069 INFO @ Tue, 16 Jun 2020 08:27:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:06: #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 08:27:06: #1 tags after filtering in treatment: 9440069 INFO @ Tue, 16 Jun 2020 08:27:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:07: #2 number of paired peaks: 566 WARNING @ Tue, 16 Jun 2020 08:27:07: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:07: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 08:27:07: #2 alternative fragment length(s) may be 110,576 bps INFO @ Tue, 16 Jun 2020 08:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.20_model.r INFO @ Tue, 16 Jun 2020 08:27:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:27:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576641/SRX2576641.20_summits.bed INFO @ Tue, 16 Jun 2020 08:27:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (601 records, 4 fields): 1 millis CompletedMACS2peakCalling