Job ID = 6452404 SRX = SRX013038 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:54:30 prefetch.2.10.7: 1) Downloading 'SRR030304'... 2020-06-21T07:54:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:55:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:55:41 prefetch.2.10.7: 'SRR030304' is valid 2020-06-21T07:55:41 prefetch.2.10.7: 1) 'SRR030304' was downloaded successfully Read 7294497 spots for SRR030304/SRR030304.sra Written 7294497 spots for SRR030304/SRR030304.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: 00:01:22 7294497 reads; of these: 7294497 (100.00%) were unpaired; of these: 403413 (5.53%) aligned 0 times 6223039 (85.31%) aligned exactly 1 time 668045 (9.16%) aligned >1 times 94.47% overall alignment rate Time searching: 00:01:22 Overall time: 00:01:22 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] 580549 / 6891084 = 0.0842 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 16:59:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.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 16:59:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:59:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:59:35: 1000000 INFO @ Sun, 21 Jun 2020 16:59:41: 2000000 INFO @ Sun, 21 Jun 2020 16:59:46: 3000000 INFO @ Sun, 21 Jun 2020 16:59:51: 4000000 INFO @ Sun, 21 Jun 2020 16:59:56: 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 @ Sun, 21 Jun 2020 17:00:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.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 17:00:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:00:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:00:02: 6000000 INFO @ Sun, 21 Jun 2020 17:00:04: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:00:04: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:00:04: #1 total tags in treatment: 6310535 INFO @ Sun, 21 Jun 2020 17:00:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:00:04: #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 17:00:04: #1 tags after filtering in treatment: 6310368 INFO @ Sun, 21 Jun 2020 17:00:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:00:04: #1 finished! INFO @ Sun, 21 Jun 2020 17:00:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:00:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:00:05: #2 number of paired peaks: 270 WARNING @ Sun, 21 Jun 2020 17:00:05: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Sun, 21 Jun 2020 17:00:05: start model_add_line... INFO @ Sun, 21 Jun 2020 17:00:05: start X-correlation... INFO @ Sun, 21 Jun 2020 17:00:05: end of X-cor INFO @ Sun, 21 Jun 2020 17:00:05: #2 finished! INFO @ Sun, 21 Jun 2020 17:00:05: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 17:00:05: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 17:00:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.05_model.r INFO @ Sun, 21 Jun 2020 17:00:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:00:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:00:05: 1000000 INFO @ Sun, 21 Jun 2020 17:00:11: 2000000 INFO @ Sun, 21 Jun 2020 17:00:16: 3000000 INFO @ Sun, 21 Jun 2020 17:00:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:00:21: 4000000 INFO @ Sun, 21 Jun 2020 17:00:27: 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 @ Sun, 21 Jun 2020 17:00:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:00:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:00:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.05_summits.bed INFO @ Sun, 21 Jun 2020 17:00:29: Done! pass1 - making usageList (76 chroms): 1 millis pass2 - checking and writing primary data (2724 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.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 17:00:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:00:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:00:32: 6000000 INFO @ Sun, 21 Jun 2020 17:00:34: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:00:34: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:00:34: #1 total tags in treatment: 6310535 INFO @ Sun, 21 Jun 2020 17:00:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:00:34: #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 17:00:35: #1 tags after filtering in treatment: 6310368 INFO @ Sun, 21 Jun 2020 17:00:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:00:35: #1 finished! INFO @ Sun, 21 Jun 2020 17:00:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:00:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:00:35: #2 number of paired peaks: 270 WARNING @ Sun, 21 Jun 2020 17:00:35: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Sun, 21 Jun 2020 17:00:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:00:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:00:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:00:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:00:35: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 17:00:35: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 17:00:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.10_model.r INFO @ Sun, 21 Jun 2020 17:00:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:00:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:00:36: 1000000 INFO @ Sun, 21 Jun 2020 17:00:41: 2000000 INFO @ Sun, 21 Jun 2020 17:00:46: 3000000 INFO @ Sun, 21 Jun 2020 17:00:51: 4000000 INFO @ Sun, 21 Jun 2020 17:00:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:00:56: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:01:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:01:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:01:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.10_summits.bed INFO @ Sun, 21 Jun 2020 17:01:00: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (659 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:01:02: 6000000 INFO @ Sun, 21 Jun 2020 17:01:04: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:01:04: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:01:04: #1 total tags in treatment: 6310535 INFO @ Sun, 21 Jun 2020 17:01:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:01:04: #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 17:01:04: #1 tags after filtering in treatment: 6310368 INFO @ Sun, 21 Jun 2020 17:01:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:01:04: #1 finished! INFO @ Sun, 21 Jun 2020 17:01:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:01:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:01:05: #2 number of paired peaks: 270 WARNING @ Sun, 21 Jun 2020 17:01:05: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Sun, 21 Jun 2020 17:01:05: start model_add_line... INFO @ Sun, 21 Jun 2020 17:01:05: start X-correlation... INFO @ Sun, 21 Jun 2020 17:01:05: end of X-cor INFO @ Sun, 21 Jun 2020 17:01:05: #2 finished! INFO @ Sun, 21 Jun 2020 17:01:05: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 17:01:05: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 17:01:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.20_model.r INFO @ Sun, 21 Jun 2020 17:01:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:01:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:01:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:01:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:01:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:01:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013038/SRX013038.20_summits.bed INFO @ Sun, 21 Jun 2020 17:01:30: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (91 records, 4 fields): 2 millis CompletedMACS2peakCalling