Job ID = 6454677 SRX = SRX2504293 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:34:10 prefetch.2.10.7: 1) Downloading 'SRR5188371'... 2020-06-21T09:34:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:34:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:34:41 prefetch.2.10.7: 'SRR5188371' is valid 2020-06-21T09:34:41 prefetch.2.10.7: 1) 'SRR5188371' was downloaded successfully 2020-06-21T09:34:46 prefetch.2.10.7: 'SRR5188371' has 0 unresolved dependencies Read 1439839 spots for SRR5188371/SRR5188371.sra Written 1439839 spots for SRR5188371/SRR5188371.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: 00:00:25 1439839 reads; of these: 1439839 (100.00%) were unpaired; of these: 2748 (0.19%) aligned 0 times 1365638 (94.85%) aligned exactly 1 time 71453 (4.96%) aligned >1 times 99.81% overall alignment rate Time searching: 00:00:25 Overall time: 00:00:25 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] 2818 / 1437091 = 0.0020 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 18:36:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.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 18:36:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:36:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:36:25: 1000000 INFO @ Sun, 21 Jun 2020 18:36:28: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:36:28: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:36:28: #1 total tags in treatment: 1434273 INFO @ Sun, 21 Jun 2020 18:36:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:28: #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 18:36:28: #1 tags after filtering in treatment: 1433525 INFO @ Sun, 21 Jun 2020 18:36:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:28: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:28: #2 number of paired peaks: 222 WARNING @ Sun, 21 Jun 2020 18:36:28: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Sun, 21 Jun 2020 18:36:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:28: #2 predicted fragment length is 192 bps INFO @ Sun, 21 Jun 2020 18:36:28: #2 alternative fragment length(s) may be 53,192,310 bps INFO @ Sun, 21 Jun 2020 18:36:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.05_model.r INFO @ Sun, 21 Jun 2020 18:36:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:36:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:36:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:36:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:36:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.05_summits.bed INFO @ Sun, 21 Jun 2020 18:36:33: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (45 records, 4 fields): 2 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 18:36:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.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 18:36:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:36:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:36:54: 1000000 INFO @ Sun, 21 Jun 2020 18:36:58: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:36:58: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:36:58: #1 total tags in treatment: 1434273 INFO @ Sun, 21 Jun 2020 18:36:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:58: #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 18:36:58: #1 tags after filtering in treatment: 1433525 INFO @ Sun, 21 Jun 2020 18:36:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:58: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:58: #2 number of paired peaks: 222 WARNING @ Sun, 21 Jun 2020 18:36:58: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Sun, 21 Jun 2020 18:36:58: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:58: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:58: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:58: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:58: #2 predicted fragment length is 192 bps INFO @ Sun, 21 Jun 2020 18:36:58: #2 alternative fragment length(s) may be 53,192,310 bps INFO @ Sun, 21 Jun 2020 18:36:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.10_model.r INFO @ Sun, 21 Jun 2020 18:36:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:37:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:37:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.10_summits.bed INFO @ Sun, 21 Jun 2020 18:37:03: Done! pass1 - making usageList (19 chroms): 0 millis pass2 - checking and writing primary data (31 records, 4 fields): 2 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 18:37:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.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 18:37:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:37:24: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:37:28: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:37:28: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:37:28: #1 total tags in treatment: 1434273 INFO @ Sun, 21 Jun 2020 18:37:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:37:28: #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 18:37:28: #1 tags after filtering in treatment: 1433525 INFO @ Sun, 21 Jun 2020 18:37:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:37:28: #1 finished! INFO @ Sun, 21 Jun 2020 18:37:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:37:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:37:28: #2 number of paired peaks: 222 WARNING @ Sun, 21 Jun 2020 18:37:28: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Sun, 21 Jun 2020 18:37:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:37:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:37:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:37:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:37:28: #2 predicted fragment length is 192 bps INFO @ Sun, 21 Jun 2020 18:37:28: #2 alternative fragment length(s) may be 53,192,310 bps INFO @ Sun, 21 Jun 2020 18:37:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.20_model.r INFO @ Sun, 21 Jun 2020 18:37:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:37:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:37:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:37:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2504293/SRX2504293.20_summits.bed INFO @ Sun, 21 Jun 2020 18:37:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (23 records, 4 fields): 2 millis CompletedMACS2peakCalling