Job ID = 6454544 SRX = SRX231857 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:20:09 prefetch.2.10.7: 1) Downloading 'SRR696672'... 2020-06-21T09:20:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:21:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:21:13 prefetch.2.10.7: 'SRR696672' is valid 2020-06-21T09:21:13 prefetch.2.10.7: 1) 'SRR696672' was downloaded successfully Read 3313650 spots for SRR696672/SRR696672.sra Written 3313650 spots for SRR696672/SRR696672.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: 00:00:26 3313650 reads; of these: 3313650 (100.00%) were unpaired; of these: 1157014 (34.92%) aligned 0 times 2013396 (60.76%) aligned exactly 1 time 143240 (4.32%) aligned >1 times 65.08% overall alignment rate Time searching: 00:00:26 Overall time: 00:00:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 177203 / 2156636 = 0.0822 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 @ Sun, 21 Jun 2020 18:22:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:22:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:22:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:22:50: 1000000 INFO @ Sun, 21 Jun 2020 18:22:55: #1 tag size is determined as 34 bps INFO @ Sun, 21 Jun 2020 18:22:55: #1 tag size = 34 INFO @ Sun, 21 Jun 2020 18:22:55: #1 total tags in treatment: 1979433 INFO @ Sun, 21 Jun 2020 18:22:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:22:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:22:56: #1 tags after filtering in treatment: 1978673 INFO @ Sun, 21 Jun 2020 18:22:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:22:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:22:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:22:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:22:56: #2 number of paired peaks: 468 WARNING @ Sun, 21 Jun 2020 18:22:56: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sun, 21 Jun 2020 18:22:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:22:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:22:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:22:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:22:56: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 18:22:56: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 18:22:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.05_model.r INFO @ Sun, 21 Jun 2020 18:22:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:22:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:23:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.05_summits.bed INFO @ Sun, 21 Jun 2020 18:23:04: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (789 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 @ Sun, 21 Jun 2020 18:23:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:23:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:23:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:23:20: 1000000 INFO @ Sun, 21 Jun 2020 18:23:25: #1 tag size is determined as 34 bps INFO @ Sun, 21 Jun 2020 18:23:25: #1 tag size = 34 INFO @ Sun, 21 Jun 2020 18:23:25: #1 total tags in treatment: 1979433 INFO @ Sun, 21 Jun 2020 18:23:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:23:25: #1 tags after filtering in treatment: 1978673 INFO @ Sun, 21 Jun 2020 18:23:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:25: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:26: #2 number of paired peaks: 468 WARNING @ Sun, 21 Jun 2020 18:23:26: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sun, 21 Jun 2020 18:23:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:26: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 18:23:26: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 18:23:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.10_model.r INFO @ Sun, 21 Jun 2020 18:23:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:23:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.10_summits.bed INFO @ Sun, 21 Jun 2020 18:23:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (121 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Sun, 21 Jun 2020 18:23:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 18:23:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:23:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:23:51: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:23:56: #1 tag size is determined as 34 bps INFO @ Sun, 21 Jun 2020 18:23:56: #1 tag size = 34 INFO @ Sun, 21 Jun 2020 18:23:56: #1 total tags in treatment: 1979433 INFO @ Sun, 21 Jun 2020 18:23:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:23:57: #1 tags after filtering in treatment: 1978673 INFO @ Sun, 21 Jun 2020 18:23:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:57: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:57: #2 number of paired peaks: 468 WARNING @ Sun, 21 Jun 2020 18:23:57: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sun, 21 Jun 2020 18:23:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:57: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 18:23:57: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 18:23:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.20_model.r INFO @ Sun, 21 Jun 2020 18:23:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:24:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231857/SRX231857.20_summits.bed INFO @ Sun, 21 Jun 2020 18:24:04: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 2 millis CompletedMACS2peakCalling