Job ID = 6452423 SRX = SRX013048 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:49:45 prefetch.2.10.7: 1) Downloading 'SRR030314'... 2020-06-21T07:49:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:50:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:50:44 prefetch.2.10.7: 'SRR030314' is valid 2020-06-21T07:50:44 prefetch.2.10.7: 1) 'SRR030314' was downloaded successfully Read 2104722 spots for SRR030314/SRR030314.sra Written 2104722 spots for SRR030314/SRR030314.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: 00:00:30 2104722 reads; of these: 2104722 (100.00%) were unpaired; of these: 312299 (14.84%) aligned 0 times 1395621 (66.31%) aligned exactly 1 time 396802 (18.85%) aligned >1 times 85.16% overall alignment rate Time searching: 00:00:30 Overall time: 00:00:30 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] 199881 / 1792423 = 0.1115 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 16:52:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.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 16:52:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:52:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:52:27: 1000000 INFO @ Sun, 21 Jun 2020 16:52:31: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:52:31: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:52:31: #1 total tags in treatment: 1592542 INFO @ Sun, 21 Jun 2020 16:52:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:52:31: #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 16:52:32: #1 tags after filtering in treatment: 1591953 INFO @ Sun, 21 Jun 2020 16:52:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:52:32: #1 finished! INFO @ Sun, 21 Jun 2020 16:52:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:52:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:52:32: #2 number of paired peaks: 987 WARNING @ Sun, 21 Jun 2020 16:52:32: Fewer paired peaks (987) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 987 pairs to build model! INFO @ Sun, 21 Jun 2020 16:52:32: start model_add_line... INFO @ Sun, 21 Jun 2020 16:52:32: start X-correlation... INFO @ Sun, 21 Jun 2020 16:52:32: end of X-cor INFO @ Sun, 21 Jun 2020 16:52:32: #2 finished! INFO @ Sun, 21 Jun 2020 16:52:32: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 16:52:32: #2 alternative fragment length(s) may be 79,113,587 bps INFO @ Sun, 21 Jun 2020 16:52:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.05_model.r INFO @ Sun, 21 Jun 2020 16:52:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:52:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:52:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:52:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:52:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.05_summits.bed INFO @ Sun, 21 Jun 2020 16:52:38: Done! pass1 - making usageList (179 chroms): 1 millis pass2 - checking and writing primary data (478 records, 4 fields): 7 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 16:52:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.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 16:52:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:52:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:52:57: 1000000 INFO @ Sun, 21 Jun 2020 16:53:01: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:53:01: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:53:01: #1 total tags in treatment: 1592542 INFO @ Sun, 21 Jun 2020 16:53:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:53:01: #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 16:53:01: #1 tags after filtering in treatment: 1591953 INFO @ Sun, 21 Jun 2020 16:53:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:53:01: #1 finished! INFO @ Sun, 21 Jun 2020 16:53:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:53:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:53:02: #2 number of paired peaks: 987 WARNING @ Sun, 21 Jun 2020 16:53:02: Fewer paired peaks (987) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 987 pairs to build model! INFO @ Sun, 21 Jun 2020 16:53:02: start model_add_line... INFO @ Sun, 21 Jun 2020 16:53:02: start X-correlation... INFO @ Sun, 21 Jun 2020 16:53:02: end of X-cor INFO @ Sun, 21 Jun 2020 16:53:02: #2 finished! INFO @ Sun, 21 Jun 2020 16:53:02: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 16:53:02: #2 alternative fragment length(s) may be 79,113,587 bps INFO @ Sun, 21 Jun 2020 16:53:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.10_model.r INFO @ Sun, 21 Jun 2020 16:53:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:53:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:53:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:53:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:53:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:53:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.10_summits.bed INFO @ Sun, 21 Jun 2020 16:53:08: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (135 records, 4 fields): 5 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 16:53:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.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 16:53:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:53:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:53:27: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:53:31: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:53:31: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:53:31: #1 total tags in treatment: 1592542 INFO @ Sun, 21 Jun 2020 16:53:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:53:31: #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 16:53:31: #1 tags after filtering in treatment: 1591953 INFO @ Sun, 21 Jun 2020 16:53:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:53:31: #1 finished! INFO @ Sun, 21 Jun 2020 16:53:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:53:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:53:31: #2 number of paired peaks: 987 WARNING @ Sun, 21 Jun 2020 16:53:31: Fewer paired peaks (987) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 987 pairs to build model! INFO @ Sun, 21 Jun 2020 16:53:31: start model_add_line... INFO @ Sun, 21 Jun 2020 16:53:31: start X-correlation... INFO @ Sun, 21 Jun 2020 16:53:32: end of X-cor INFO @ Sun, 21 Jun 2020 16:53:32: #2 finished! INFO @ Sun, 21 Jun 2020 16:53:32: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 16:53:32: #2 alternative fragment length(s) may be 79,113,587 bps INFO @ Sun, 21 Jun 2020 16:53:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.20_model.r INFO @ Sun, 21 Jun 2020 16:53:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:53:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:53:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:53:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:53:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:53:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013048/SRX013048.20_summits.bed INFO @ Sun, 21 Jun 2020 16:53:38: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (67 records, 4 fields): 3 millis CompletedMACS2peakCalling