Job ID = 6455697 SRX = SRX287998 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:13:36 prefetch.2.10.7: 1) Downloading 'SRR870187'... 2020-06-21T10:13:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:15:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:15:41 prefetch.2.10.7: 'SRR870187' is valid 2020-06-21T10:15:41 prefetch.2.10.7: 1) 'SRR870187' was downloaded successfully Read 10268681 spots for SRR870187/SRR870187.sra Written 10268681 spots for SRR870187/SRR870187.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:22 10268681 reads; of these: 10268681 (100.00%) were unpaired; of these: 668210 (6.51%) aligned 0 times 8224861 (80.10%) aligned exactly 1 time 1375610 (13.40%) aligned >1 times 93.49% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 594664 / 9600471 = 0.0619 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 19:21:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.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 19:21:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:21:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:21:38: 1000000 INFO @ Sun, 21 Jun 2020 19:21:44: 2000000 INFO @ Sun, 21 Jun 2020 19:21:49: 3000000 INFO @ Sun, 21 Jun 2020 19:21:55: 4000000 INFO @ Sun, 21 Jun 2020 19:22:00: 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 19:22:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.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 19:22:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:06: 6000000 INFO @ Sun, 21 Jun 2020 19:22:09: 1000000 INFO @ Sun, 21 Jun 2020 19:22:12: 7000000 INFO @ Sun, 21 Jun 2020 19:22:15: 2000000 INFO @ Sun, 21 Jun 2020 19:22:18: 8000000 INFO @ Sun, 21 Jun 2020 19:22:20: 3000000 INFO @ Sun, 21 Jun 2020 19:22:24: 9000000 INFO @ Sun, 21 Jun 2020 19:22:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:22:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:22:25: #1 total tags in treatment: 9005807 INFO @ Sun, 21 Jun 2020 19:22:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:22:25: #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 19:22:25: #1 tags after filtering in treatment: 9005802 INFO @ Sun, 21 Jun 2020 19:22:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:22:25: #1 finished! INFO @ Sun, 21 Jun 2020 19:22:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:22:26: #2 number of paired peaks: 597 WARNING @ Sun, 21 Jun 2020 19:22:26: Fewer paired peaks (597) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 597 pairs to build model! INFO @ Sun, 21 Jun 2020 19:22:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:22:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:22:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:22:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:22:26: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 19:22:26: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 19:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.05_model.r INFO @ Sun, 21 Jun 2020 19:22:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:22:26: 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 19:22:32: 5000000 INFO @ Sun, 21 Jun 2020 19:22:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.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 19:22:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:38: 6000000 INFO @ Sun, 21 Jun 2020 19:22:40: 1000000 INFO @ Sun, 21 Jun 2020 19:22:44: 7000000 INFO @ Sun, 21 Jun 2020 19:22:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:22:47: 2000000 INFO @ Sun, 21 Jun 2020 19:22:51: 8000000 INFO @ Sun, 21 Jun 2020 19:22:53: 3000000 INFO @ Sun, 21 Jun 2020 19:22:58: 9000000 INFO @ Sun, 21 Jun 2020 19:22:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:22:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:22:58: #1 total tags in treatment: 9005807 INFO @ Sun, 21 Jun 2020 19:22:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:22:58: #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 19:22:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:22:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:22:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.05_summits.bed INFO @ Sun, 21 Jun 2020 19:22:58: Done! INFO @ Sun, 21 Jun 2020 19:22:58: #1 tags after filtering in treatment: 9005802 INFO @ Sun, 21 Jun 2020 19:22:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:22:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:22:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:22:58: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (410 chroms): 2 millis pass2 - checking and writing primary data (6000 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:22:59: #2 number of paired peaks: 597 WARNING @ Sun, 21 Jun 2020 19:22:59: Fewer paired peaks (597) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 597 pairs to build model! INFO @ Sun, 21 Jun 2020 19:22:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:22:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:22:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:22:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:22:59: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 19:22:59: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 19:22:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.10_model.r INFO @ Sun, 21 Jun 2020 19:22:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:22:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:00: 4000000 INFO @ Sun, 21 Jun 2020 19:23:06: 5000000 INFO @ Sun, 21 Jun 2020 19:23:12: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:23:18: 7000000 INFO @ Sun, 21 Jun 2020 19:23:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:23:25: 8000000 INFO @ Sun, 21 Jun 2020 19:23:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:23:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:23:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.10_summits.bed INFO @ Sun, 21 Jun 2020 19:23:29: Done! pass1 - making usageList (274 chroms): 1 millis pass2 - checking and writing primary data (3563 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:23:31: 9000000 INFO @ Sun, 21 Jun 2020 19:23:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:23:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:23:31: #1 total tags in treatment: 9005807 INFO @ Sun, 21 Jun 2020 19:23:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:31: #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 19:23:32: #1 tags after filtering in treatment: 9005802 INFO @ Sun, 21 Jun 2020 19:23:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:32: #2 number of paired peaks: 597 WARNING @ Sun, 21 Jun 2020 19:23:32: Fewer paired peaks (597) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 597 pairs to build model! INFO @ Sun, 21 Jun 2020 19:23:32: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:32: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:32: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:32: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:32: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 19:23:32: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 19:23:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.20_model.r INFO @ Sun, 21 Jun 2020 19:23:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:23:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287998/SRX287998.20_summits.bed INFO @ Sun, 21 Jun 2020 19:24:02: Done! pass1 - making usageList (111 chroms): 1 millis pass2 - checking and writing primary data (1330 records, 4 fields): 7 millis CompletedMACS2peakCalling