Job ID = 6452518 SRX = SRX013115 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:41:36 prefetch.2.10.7: 1) Downloading 'SRR030381'... 2020-06-21T07:41:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:42:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:42:35 prefetch.2.10.7: 'SRR030381' is valid 2020-06-21T07:42:35 prefetch.2.10.7: 1) 'SRR030381' was downloaded successfully Read 3213218 spots for SRR030381/SRR030381.sra Written 3213218 spots for SRR030381/SRR030381.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: 00:00:36 3213218 reads; of these: 3213218 (100.00%) were unpaired; of these: 154942 (4.82%) aligned 0 times 2607665 (81.15%) aligned exactly 1 time 450611 (14.02%) aligned >1 times 95.18% overall alignment rate Time searching: 00:00:36 Overall time: 00:00:36 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] 274859 / 3058276 = 0.0899 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 16:44:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.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 16:44:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:44:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:44:39: 1000000 INFO @ Sun, 21 Jun 2020 16:44:43: 2000000 INFO @ Sun, 21 Jun 2020 16:44:48: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:44:48: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:44:48: #1 total tags in treatment: 2783417 INFO @ Sun, 21 Jun 2020 16:44:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:44:48: #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 16:44:48: #1 tags after filtering in treatment: 2783193 INFO @ Sun, 21 Jun 2020 16:44:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:44:48: #1 finished! INFO @ Sun, 21 Jun 2020 16:44:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:44:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:44:48: #2 number of paired peaks: 659 WARNING @ Sun, 21 Jun 2020 16:44:48: Fewer paired peaks (659) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 659 pairs to build model! INFO @ Sun, 21 Jun 2020 16:44:48: start model_add_line... INFO @ Sun, 21 Jun 2020 16:44:48: start X-correlation... INFO @ Sun, 21 Jun 2020 16:44:48: end of X-cor INFO @ Sun, 21 Jun 2020 16:44:48: #2 finished! INFO @ Sun, 21 Jun 2020 16:44:48: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 16:44:48: #2 alternative fragment length(s) may be 138 bps INFO @ Sun, 21 Jun 2020 16:44:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.05_model.r INFO @ Sun, 21 Jun 2020 16:44:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:44:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:44:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:44:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:44:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:44:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.05_summits.bed INFO @ Sun, 21 Jun 2020 16:44:58: Done! pass1 - making usageList (73 chroms): 1 millis pass2 - checking and writing primary data (1496 records, 4 fields): 4 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 16:45:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.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 16:45:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:45:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:45:09: 1000000 INFO @ Sun, 21 Jun 2020 16:45:13: 2000000 INFO @ Sun, 21 Jun 2020 16:45:18: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:45:18: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:45:18: #1 total tags in treatment: 2783417 INFO @ Sun, 21 Jun 2020 16:45:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:45:18: #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 16:45:18: #1 tags after filtering in treatment: 2783193 INFO @ Sun, 21 Jun 2020 16:45:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:45:18: #1 finished! INFO @ Sun, 21 Jun 2020 16:45:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:45:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:45:18: #2 number of paired peaks: 659 WARNING @ Sun, 21 Jun 2020 16:45:18: Fewer paired peaks (659) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 659 pairs to build model! INFO @ Sun, 21 Jun 2020 16:45:18: start model_add_line... INFO @ Sun, 21 Jun 2020 16:45:18: start X-correlation... INFO @ Sun, 21 Jun 2020 16:45:18: end of X-cor INFO @ Sun, 21 Jun 2020 16:45:18: #2 finished! INFO @ Sun, 21 Jun 2020 16:45:18: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 16:45:18: #2 alternative fragment length(s) may be 138 bps INFO @ Sun, 21 Jun 2020 16:45:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.10_model.r INFO @ Sun, 21 Jun 2020 16:45:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:45:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:45:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:45:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:45:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:45:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.10_summits.bed INFO @ Sun, 21 Jun 2020 16:45:28: Done! pass1 - making usageList (51 chroms): 0 millis pass2 - checking and writing primary data (433 records, 4 fields): 3 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 16:45:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.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 16:45:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:45:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:45:39: 1000000 INFO @ Sun, 21 Jun 2020 16:45:43: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:45:48: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:45:48: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:45:48: #1 total tags in treatment: 2783417 INFO @ Sun, 21 Jun 2020 16:45:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:45:48: #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 16:45:48: #1 tags after filtering in treatment: 2783193 INFO @ Sun, 21 Jun 2020 16:45:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:45:48: #1 finished! INFO @ Sun, 21 Jun 2020 16:45:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:45:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:45:48: #2 number of paired peaks: 659 WARNING @ Sun, 21 Jun 2020 16:45:48: Fewer paired peaks (659) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 659 pairs to build model! INFO @ Sun, 21 Jun 2020 16:45:48: start model_add_line... INFO @ Sun, 21 Jun 2020 16:45:48: start X-correlation... INFO @ Sun, 21 Jun 2020 16:45:48: end of X-cor INFO @ Sun, 21 Jun 2020 16:45:48: #2 finished! INFO @ Sun, 21 Jun 2020 16:45:48: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 16:45:48: #2 alternative fragment length(s) may be 138 bps INFO @ Sun, 21 Jun 2020 16:45:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.20_model.r INFO @ Sun, 21 Jun 2020 16:45:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:45:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:45:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:45:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:45:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:45:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013115/SRX013115.20_summits.bed INFO @ Sun, 21 Jun 2020 16:45:58: Done! pass1 - making usageList (35 chroms): 0 millis pass2 - checking and writing primary data (94 records, 4 fields): 2 millis CompletedMACS2peakCalling