Job ID = 6452697 SRX = SRX026738 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:11:48 prefetch.2.10.7: 1) Downloading 'SRR065624'... 2020-06-21T08:11:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:15:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:15:44 prefetch.2.10.7: 'SRR065624' is valid 2020-06-21T08:15:44 prefetch.2.10.7: 1) 'SRR065624' was downloaded successfully Read 13982411 spots for SRR065624/SRR065624.sra Written 13982411 spots for SRR065624/SRR065624.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: 00:01:45 13982411 reads; of these: 13982411 (100.00%) were unpaired; of these: 7684278 (54.96%) aligned 0 times 5084383 (36.36%) aligned exactly 1 time 1213750 (8.68%) aligned >1 times 45.04% overall alignment rate Time searching: 00:01:45 Overall time: 00:01:45 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] 960260 / 6298133 = 0.1525 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 17:19:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.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 17:19:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:19:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:20:03: 1000000 INFO @ Sun, 21 Jun 2020 17:20:09: 2000000 INFO @ Sun, 21 Jun 2020 17:20:15: 3000000 INFO @ Sun, 21 Jun 2020 17:20:21: 4000000 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 17:20:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.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 17:20:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:20:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:20:28: 5000000 INFO @ Sun, 21 Jun 2020 17:20:31: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:20:31: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:20:31: #1 total tags in treatment: 5337873 INFO @ Sun, 21 Jun 2020 17:20:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:20:31: #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 17:20:31: #1 tags after filtering in treatment: 5337806 INFO @ Sun, 21 Jun 2020 17:20:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:20:31: #1 finished! INFO @ Sun, 21 Jun 2020 17:20:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:20:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:20:31: #2 number of paired peaks: 412 WARNING @ Sun, 21 Jun 2020 17:20:31: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Sun, 21 Jun 2020 17:20:31: start model_add_line... INFO @ Sun, 21 Jun 2020 17:20:31: start X-correlation... INFO @ Sun, 21 Jun 2020 17:20:32: end of X-cor INFO @ Sun, 21 Jun 2020 17:20:32: #2 finished! INFO @ Sun, 21 Jun 2020 17:20:32: #2 predicted fragment length is 279 bps INFO @ Sun, 21 Jun 2020 17:20:32: #2 alternative fragment length(s) may be 279 bps INFO @ Sun, 21 Jun 2020 17:20:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.05_model.r INFO @ Sun, 21 Jun 2020 17:20:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:20:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:20:34: 1000000 INFO @ Sun, 21 Jun 2020 17:20:40: 2000000 INFO @ Sun, 21 Jun 2020 17:20:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:20:46: 3000000 INFO @ Sun, 21 Jun 2020 17:20:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:20:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:20:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.05_summits.bed INFO @ Sun, 21 Jun 2020 17:20:51: Done! pass1 - making usageList (162 chroms): 1 millis pass2 - checking and writing primary data (1874 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:20:53: 4000000 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 17:20:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.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 17:20:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:20:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:21:00: 5000000 INFO @ Sun, 21 Jun 2020 17:21:03: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:21:03: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:21:03: #1 total tags in treatment: 5337873 INFO @ Sun, 21 Jun 2020 17:21:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:21:03: #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 17:21:03: #1 tags after filtering in treatment: 5337806 INFO @ Sun, 21 Jun 2020 17:21:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:21:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:21:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:21:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:21:03: 1000000 INFO @ Sun, 21 Jun 2020 17:21:04: #2 number of paired peaks: 412 WARNING @ Sun, 21 Jun 2020 17:21:04: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Sun, 21 Jun 2020 17:21:04: start model_add_line... INFO @ Sun, 21 Jun 2020 17:21:04: start X-correlation... INFO @ Sun, 21 Jun 2020 17:21:04: end of X-cor INFO @ Sun, 21 Jun 2020 17:21:04: #2 finished! INFO @ Sun, 21 Jun 2020 17:21:04: #2 predicted fragment length is 279 bps INFO @ Sun, 21 Jun 2020 17:21:04: #2 alternative fragment length(s) may be 279 bps INFO @ Sun, 21 Jun 2020 17:21:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.10_model.r INFO @ Sun, 21 Jun 2020 17:21:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:21:08: 2000000 INFO @ Sun, 21 Jun 2020 17:21:14: 3000000 INFO @ Sun, 21 Jun 2020 17:21:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:21:19: 4000000 INFO @ Sun, 21 Jun 2020 17:21:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:21:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:21:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.10_summits.bed INFO @ Sun, 21 Jun 2020 17:21:23: Done! pass1 - making usageList (101 chroms): 1 millis pass2 - checking and writing primary data (609 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:21:25: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:21:27: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:21:27: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:21:27: #1 total tags in treatment: 5337873 INFO @ Sun, 21 Jun 2020 17:21:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:21:27: #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 17:21:27: #1 tags after filtering in treatment: 5337806 INFO @ Sun, 21 Jun 2020 17:21:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:21:27: #1 finished! INFO @ Sun, 21 Jun 2020 17:21:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:21:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:21:28: #2 number of paired peaks: 412 WARNING @ Sun, 21 Jun 2020 17:21:28: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Sun, 21 Jun 2020 17:21:28: start model_add_line... INFO @ Sun, 21 Jun 2020 17:21:28: start X-correlation... INFO @ Sun, 21 Jun 2020 17:21:28: end of X-cor INFO @ Sun, 21 Jun 2020 17:21:28: #2 finished! INFO @ Sun, 21 Jun 2020 17:21:28: #2 predicted fragment length is 279 bps INFO @ Sun, 21 Jun 2020 17:21:28: #2 alternative fragment length(s) may be 279 bps INFO @ Sun, 21 Jun 2020 17:21:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.20_model.r INFO @ Sun, 21 Jun 2020 17:21:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:21:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:21:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:21:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:21:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:21:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026738/SRX026738.20_summits.bed INFO @ Sun, 21 Jun 2020 17:21:46: Done! pass1 - making usageList (74 chroms): 1 millis pass2 - checking and writing primary data (252 records, 4 fields): 3 millis CompletedMACS2peakCalling