Job ID = 6457854 SRX = SRX4801817 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:21:53 prefetch.2.10.7: 1) Downloading 'SRR7968402'... 2020-06-21T12:21:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:23:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:23:54 prefetch.2.10.7: 'SRR7968402' is valid 2020-06-21T12:23:54 prefetch.2.10.7: 1) 'SRR7968402' was downloaded successfully Read 11648449 spots for SRR7968402/SRR7968402.sra Written 11648449 spots for SRR7968402/SRR7968402.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: 00:04:08 11648449 reads; of these: 11648449 (100.00%) were unpaired; of these: 358250 (3.08%) aligned 0 times 7970674 (68.43%) aligned exactly 1 time 3319525 (28.50%) aligned >1 times 96.92% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2574258 / 11290199 = 0.2280 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 21:32:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.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 21:32:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:33:02: 1000000 INFO @ Sun, 21 Jun 2020 21:33:07: 2000000 INFO @ Sun, 21 Jun 2020 21:33:14: 3000000 INFO @ Sun, 21 Jun 2020 21:33:20: 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 21:33:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.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 21:33:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:33:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:33:26: 5000000 INFO @ Sun, 21 Jun 2020 21:33:32: 6000000 INFO @ Sun, 21 Jun 2020 21:33:33: 1000000 INFO @ Sun, 21 Jun 2020 21:33:39: 7000000 INFO @ Sun, 21 Jun 2020 21:33:39: 2000000 INFO @ Sun, 21 Jun 2020 21:33:46: 8000000 INFO @ Sun, 21 Jun 2020 21:33:46: 3000000 INFO @ Sun, 21 Jun 2020 21:33:51: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:33:51: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:33:51: #1 total tags in treatment: 8715941 INFO @ Sun, 21 Jun 2020 21:33:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:51: #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 21:33:51: #1 tags after filtering in treatment: 8715778 INFO @ Sun, 21 Jun 2020 21:33:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:51: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:52: #2 number of paired peaks: 5069 INFO @ Sun, 21 Jun 2020 21:33:52: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:52: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:52: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:52: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:52: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 21:33:52: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 21 Jun 2020 21:33:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.05_model.r INFO @ Sun, 21 Jun 2020 21:33:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:33:53: 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 21:33:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.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 21:33:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:33:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:33:59: 5000000 INFO @ Sun, 21 Jun 2020 21:34:02: 1000000 INFO @ Sun, 21 Jun 2020 21:34:06: 6000000 INFO @ Sun, 21 Jun 2020 21:34:08: 2000000 INFO @ Sun, 21 Jun 2020 21:34:13: 7000000 INFO @ Sun, 21 Jun 2020 21:34:15: 3000000 INFO @ Sun, 21 Jun 2020 21:34:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:34:21: 8000000 INFO @ Sun, 21 Jun 2020 21:34:21: 4000000 INFO @ Sun, 21 Jun 2020 21:34:26: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:34:26: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:34:26: #1 total tags in treatment: 8715941 INFO @ Sun, 21 Jun 2020 21:34:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:34:26: #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 21:34:26: #1 tags after filtering in treatment: 8715778 INFO @ Sun, 21 Jun 2020 21:34:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:34:26: #1 finished! INFO @ Sun, 21 Jun 2020 21:34:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:34:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:34:27: 5000000 INFO @ Sun, 21 Jun 2020 21:34:27: #2 number of paired peaks: 5069 INFO @ Sun, 21 Jun 2020 21:34:27: start model_add_line... INFO @ Sun, 21 Jun 2020 21:34:27: start X-correlation... INFO @ Sun, 21 Jun 2020 21:34:27: end of X-cor INFO @ Sun, 21 Jun 2020 21:34:27: #2 finished! INFO @ Sun, 21 Jun 2020 21:34:27: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 21:34:27: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 21 Jun 2020 21:34:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.10_model.r INFO @ Sun, 21 Jun 2020 21:34:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:34:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:34:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:34:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:34:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.05_summits.bed INFO @ Sun, 21 Jun 2020 21:34:30: Done! pass1 - making usageList (539 chroms): 2 millis pass2 - checking and writing primary data (8523 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:34:33: 6000000 INFO @ Sun, 21 Jun 2020 21:34:39: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:34:46: 8000000 INFO @ Sun, 21 Jun 2020 21:34:51: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:34:51: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:34:51: #1 total tags in treatment: 8715941 INFO @ Sun, 21 Jun 2020 21:34:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:34:51: #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 21:34:51: #1 tags after filtering in treatment: 8715778 INFO @ Sun, 21 Jun 2020 21:34:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:34:51: #1 finished! INFO @ Sun, 21 Jun 2020 21:34:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:34:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:34:52: #2 number of paired peaks: 5069 INFO @ Sun, 21 Jun 2020 21:34:52: start model_add_line... INFO @ Sun, 21 Jun 2020 21:34:52: start X-correlation... INFO @ Sun, 21 Jun 2020 21:34:52: end of X-cor INFO @ Sun, 21 Jun 2020 21:34:52: #2 finished! INFO @ Sun, 21 Jun 2020 21:34:52: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 21:34:52: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 21 Jun 2020 21:34:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.20_model.r INFO @ Sun, 21 Jun 2020 21:34:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:34:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:34:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.10_summits.bed INFO @ Sun, 21 Jun 2020 21:35:04: Done! pass1 - making usageList (435 chroms): 2 millis pass2 - checking and writing primary data (6988 records, 4 fields): 33 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:35:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801817/SRX4801817.20_summits.bed INFO @ Sun, 21 Jun 2020 21:35:29: Done! pass1 - making usageList (254 chroms): 2 millis pass2 - checking and writing primary data (5215 records, 4 fields): 22 millis CompletedMACS2peakCalling