Job ID = 6368221 SRX = SRX494904 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:11:35 prefetch.2.10.7: 1) Downloading 'SRR1198436'... 2020-06-16T00:11:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:15:47 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:15:47 prefetch.2.10.7: 1) 'SRR1198436' was downloaded successfully Read 26790193 spots for SRR1198436/SRR1198436.sra Written 26790193 spots for SRR1198436/SRR1198436.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: 00:06:06 26790193 reads; of these: 26790193 (100.00%) were unpaired; of these: 2345581 (8.76%) aligned 0 times 20142984 (75.19%) aligned exactly 1 time 4301628 (16.06%) aligned >1 times 91.24% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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] 14430114 / 24444612 = 0.5903 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 09:28:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.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 09:28:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:25: 1000000 INFO @ Tue, 16 Jun 2020 09:28:30: 2000000 INFO @ Tue, 16 Jun 2020 09:28:36: 3000000 INFO @ Tue, 16 Jun 2020 09:28:41: 4000000 INFO @ Tue, 16 Jun 2020 09:28:46: 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 09:28:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.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 09:28:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:51: 6000000 INFO @ Tue, 16 Jun 2020 09:28:56: 1000000 INFO @ Tue, 16 Jun 2020 09:28:57: 7000000 INFO @ Tue, 16 Jun 2020 09:29:01: 2000000 INFO @ Tue, 16 Jun 2020 09:29:02: 8000000 INFO @ Tue, 16 Jun 2020 09:29:07: 3000000 INFO @ Tue, 16 Jun 2020 09:29:08: 9000000 INFO @ Tue, 16 Jun 2020 09:29:12: 4000000 INFO @ Tue, 16 Jun 2020 09:29:14: 10000000 INFO @ Tue, 16 Jun 2020 09:29:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:29:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:29:14: #1 total tags in treatment: 10014498 INFO @ Tue, 16 Jun 2020 09:29:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:14: #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 09:29:14: #1 tags after filtering in treatment: 10014498 INFO @ Tue, 16 Jun 2020 09:29:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:15: #2 number of paired peaks: 930 WARNING @ Tue, 16 Jun 2020 09:29:15: Fewer paired peaks (930) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 930 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:15: #2 predicted fragment length is 118 bps INFO @ Tue, 16 Jun 2020 09:29:15: #2 alternative fragment length(s) may be 118,597 bps INFO @ Tue, 16 Jun 2020 09:29:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.05_model.r INFO @ Tue, 16 Jun 2020 09:29:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:18: 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 09:29:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.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 09:29:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:23: 6000000 INFO @ Tue, 16 Jun 2020 09:29:27: 1000000 INFO @ Tue, 16 Jun 2020 09:29:29: 7000000 INFO @ Tue, 16 Jun 2020 09:29:33: 2000000 INFO @ Tue, 16 Jun 2020 09:29:34: 8000000 INFO @ Tue, 16 Jun 2020 09:29:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:38: 3000000 INFO @ Tue, 16 Jun 2020 09:29:40: 9000000 INFO @ Tue, 16 Jun 2020 09:29:44: 4000000 INFO @ Tue, 16 Jun 2020 09:29:45: 10000000 INFO @ Tue, 16 Jun 2020 09:29:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:29:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:29:46: #1 total tags in treatment: 10014498 INFO @ Tue, 16 Jun 2020 09:29:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:46: #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 09:29:46: #1 tags after filtering in treatment: 10014498 INFO @ Tue, 16 Jun 2020 09:29:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:47: #2 number of paired peaks: 930 WARNING @ Tue, 16 Jun 2020 09:29:47: Fewer paired peaks (930) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 930 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:47: #2 predicted fragment length is 118 bps INFO @ Tue, 16 Jun 2020 09:29:47: #2 alternative fragment length(s) may be 118,597 bps INFO @ Tue, 16 Jun 2020 09:29:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.10_model.r INFO @ Tue, 16 Jun 2020 09:29:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:49: 5000000 INFO @ Tue, 16 Jun 2020 09:29:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.05_summits.bed INFO @ Tue, 16 Jun 2020 09:29:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5369 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:54: 6000000 INFO @ Tue, 16 Jun 2020 09:30:00: 7000000 INFO @ Tue, 16 Jun 2020 09:30:05: 8000000 INFO @ Tue, 16 Jun 2020 09:30:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:10: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:30:16: 10000000 INFO @ Tue, 16 Jun 2020 09:30:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:30:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:30:16: #1 total tags in treatment: 10014498 INFO @ Tue, 16 Jun 2020 09:30:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:16: #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 09:30:16: #1 tags after filtering in treatment: 10014498 INFO @ Tue, 16 Jun 2020 09:30:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:17: #2 number of paired peaks: 930 WARNING @ Tue, 16 Jun 2020 09:30:17: Fewer paired peaks (930) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 930 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:17: #2 predicted fragment length is 118 bps INFO @ Tue, 16 Jun 2020 09:30:17: #2 alternative fragment length(s) may be 118,597 bps INFO @ Tue, 16 Jun 2020 09:30:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.20_model.r INFO @ Tue, 16 Jun 2020 09:30:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.10_summits.bed INFO @ Tue, 16 Jun 2020 09:30:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3414 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:30:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494904/SRX494904.20_summits.bed INFO @ Tue, 16 Jun 2020 09:30:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1792 records, 4 fields): 3 millis CompletedMACS2peakCalling