Job ID = 6508481 SRX = SRX287903 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:04:59 prefetch.2.10.7: 1) Downloading 'SRR870092'... 2020-06-26T14:04:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:06:52 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:06:52 prefetch.2.10.7: 1) 'SRR870092' was downloaded successfully Read 17337186 spots for SRR870092/SRR870092.sra Written 17337186 spots for SRR870092/SRR870092.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: 00:05:14 17337186 reads; of these: 17337186 (100.00%) were unpaired; of these: 961586 (5.55%) aligned 0 times 12405943 (71.56%) aligned exactly 1 time 3969657 (22.90%) aligned >1 times 94.45% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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] 1772454 / 16375600 = 0.1082 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 @ Fri, 26 Jun 2020 23:17:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.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 @ Fri, 26 Jun 2020 23:17:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:17:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:18:00: 1000000 INFO @ Fri, 26 Jun 2020 23:18:06: 2000000 INFO @ Fri, 26 Jun 2020 23:18:12: 3000000 INFO @ Fri, 26 Jun 2020 23:18:18: 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 @ Fri, 26 Jun 2020 23:18:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.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 @ Fri, 26 Jun 2020 23:18:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:18:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:18:24: 5000000 INFO @ Fri, 26 Jun 2020 23:18:30: 6000000 INFO @ Fri, 26 Jun 2020 23:18:30: 1000000 INFO @ Fri, 26 Jun 2020 23:18:36: 7000000 INFO @ Fri, 26 Jun 2020 23:18:37: 2000000 INFO @ Fri, 26 Jun 2020 23:18:43: 8000000 INFO @ Fri, 26 Jun 2020 23:18:43: 3000000 INFO @ Fri, 26 Jun 2020 23:18:50: 4000000 INFO @ Fri, 26 Jun 2020 23:18:50: 9000000 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 @ Fri, 26 Jun 2020 23:18:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.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 @ Fri, 26 Jun 2020 23:18:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:18:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:18:56: 5000000 INFO @ Fri, 26 Jun 2020 23:18:57: 10000000 INFO @ Fri, 26 Jun 2020 23:19:00: 1000000 INFO @ Fri, 26 Jun 2020 23:19:03: 6000000 INFO @ Fri, 26 Jun 2020 23:19:04: 11000000 INFO @ Fri, 26 Jun 2020 23:19:07: 2000000 INFO @ Fri, 26 Jun 2020 23:19:09: 7000000 INFO @ Fri, 26 Jun 2020 23:19:11: 12000000 INFO @ Fri, 26 Jun 2020 23:19:13: 3000000 INFO @ Fri, 26 Jun 2020 23:19:16: 8000000 INFO @ Fri, 26 Jun 2020 23:19:17: 13000000 INFO @ Fri, 26 Jun 2020 23:19:20: 4000000 INFO @ Fri, 26 Jun 2020 23:19:22: 9000000 INFO @ Fri, 26 Jun 2020 23:19:24: 14000000 INFO @ Fri, 26 Jun 2020 23:19:26: 5000000 INFO @ Fri, 26 Jun 2020 23:19:28: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:19:28: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:19:28: #1 total tags in treatment: 14603146 INFO @ Fri, 26 Jun 2020 23:19:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:19:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:19:29: #1 tags after filtering in treatment: 14603146 INFO @ Fri, 26 Jun 2020 23:19:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:19:29: #1 finished! INFO @ Fri, 26 Jun 2020 23:19:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:19:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:19:29: 10000000 INFO @ Fri, 26 Jun 2020 23:19:30: #2 number of paired peaks: 563 WARNING @ Fri, 26 Jun 2020 23:19:30: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Fri, 26 Jun 2020 23:19:30: start model_add_line... INFO @ Fri, 26 Jun 2020 23:19:30: start X-correlation... INFO @ Fri, 26 Jun 2020 23:19:30: end of X-cor INFO @ Fri, 26 Jun 2020 23:19:30: #2 finished! INFO @ Fri, 26 Jun 2020 23:19:30: #2 predicted fragment length is 137 bps INFO @ Fri, 26 Jun 2020 23:19:30: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 26 Jun 2020 23:19:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.05_model.r INFO @ Fri, 26 Jun 2020 23:19:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:19:33: 6000000 INFO @ Fri, 26 Jun 2020 23:19:35: 11000000 INFO @ Fri, 26 Jun 2020 23:19:39: 7000000 INFO @ Fri, 26 Jun 2020 23:19:42: 12000000 INFO @ Fri, 26 Jun 2020 23:19:46: 8000000 INFO @ Fri, 26 Jun 2020 23:19:48: 13000000 INFO @ Fri, 26 Jun 2020 23:19:52: 9000000 INFO @ Fri, 26 Jun 2020 23:19:54: 14000000 INFO @ Fri, 26 Jun 2020 23:19:58: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:19:58: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:19:58: #1 total tags in treatment: 14603146 INFO @ Fri, 26 Jun 2020 23:19:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:19:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:19:59: 10000000 INFO @ Fri, 26 Jun 2020 23:19:59: #1 tags after filtering in treatment: 14603146 INFO @ Fri, 26 Jun 2020 23:19:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:19:59: #1 finished! INFO @ Fri, 26 Jun 2020 23:19:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:20:00: #2 number of paired peaks: 563 WARNING @ Fri, 26 Jun 2020 23:20:00: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Fri, 26 Jun 2020 23:20:00: start model_add_line... INFO @ Fri, 26 Jun 2020 23:20:00: start X-correlation... INFO @ Fri, 26 Jun 2020 23:20:00: end of X-cor INFO @ Fri, 26 Jun 2020 23:20:00: #2 finished! INFO @ Fri, 26 Jun 2020 23:20:00: #2 predicted fragment length is 137 bps INFO @ Fri, 26 Jun 2020 23:20:00: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 26 Jun 2020 23:20:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.10_model.r INFO @ Fri, 26 Jun 2020 23:20:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:20:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:20:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:20:05: 11000000 INFO @ Fri, 26 Jun 2020 23:20:11: 12000000 INFO @ Fri, 26 Jun 2020 23:20:17: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:20:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:20:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:20:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.05_summits.bed INFO @ Fri, 26 Jun 2020 23:20:21: Done! pass1 - making usageList (641 chroms): 1 millis pass2 - checking and writing primary data (4442 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:20:23: 14000000 INFO @ Fri, 26 Jun 2020 23:20:27: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:20:27: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:20:27: #1 total tags in treatment: 14603146 INFO @ Fri, 26 Jun 2020 23:20:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:20:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:20:28: #1 tags after filtering in treatment: 14603146 INFO @ Fri, 26 Jun 2020 23:20:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:20:28: #1 finished! INFO @ Fri, 26 Jun 2020 23:20:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:20:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:20:29: #2 number of paired peaks: 563 WARNING @ Fri, 26 Jun 2020 23:20:29: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Fri, 26 Jun 2020 23:20:29: start model_add_line... INFO @ Fri, 26 Jun 2020 23:20:29: start X-correlation... INFO @ Fri, 26 Jun 2020 23:20:29: end of X-cor INFO @ Fri, 26 Jun 2020 23:20:29: #2 finished! INFO @ Fri, 26 Jun 2020 23:20:29: #2 predicted fragment length is 137 bps INFO @ Fri, 26 Jun 2020 23:20:29: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 26 Jun 2020 23:20:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.20_model.r INFO @ Fri, 26 Jun 2020 23:20:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:20:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:20:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:20:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:20:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:20:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.10_summits.bed INFO @ Fri, 26 Jun 2020 23:20:50: Done! pass1 - making usageList (557 chroms): 2 millis pass2 - checking and writing primary data (2966 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:21:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:21:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:21:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:21:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287903/SRX287903.20_summits.bed INFO @ Fri, 26 Jun 2020 23:21:18: Done! pass1 - making usageList (425 chroms): 1 millis pass2 - checking and writing primary data (1850 records, 4 fields): 15 millis CompletedMACS2peakCalling