Job ID = 6457526 SRX = SRX4669019 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:53:34 prefetch.2.10.7: 1) Downloading 'SRR7817544'... 2020-06-21T11:53:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:55:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:55:57 prefetch.2.10.7: 'SRR7817544' is valid 2020-06-21T11:55:57 prefetch.2.10.7: 1) 'SRR7817544' was downloaded successfully 2020-06-21T11:55:57 prefetch.2.10.7: 'SRR7817544' has 0 unresolved dependencies Read 23209502 spots for SRR7817544/SRR7817544.sra Written 23209502 spots for SRR7817544/SRR7817544.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: 00:04:55 23209502 reads; of these: 23209502 (100.00%) were unpaired; of these: 4627060 (19.94%) aligned 0 times 15668112 (67.51%) aligned exactly 1 time 2914330 (12.56%) aligned >1 times 80.06% overall alignment rate Time searching: 00:04:55 Overall time: 00:04:55 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] 11351979 / 18582442 = 0.6109 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 21:05:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.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 21:05:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:05:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:05:19: 1000000 INFO @ Sun, 21 Jun 2020 21:05:25: 2000000 INFO @ Sun, 21 Jun 2020 21:05:32: 3000000 INFO @ Sun, 21 Jun 2020 21:05:38: 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 21:05:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.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 21:05:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:05:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:05:45: 5000000 INFO @ Sun, 21 Jun 2020 21:05:50: 1000000 INFO @ Sun, 21 Jun 2020 21:05:52: 6000000 INFO @ Sun, 21 Jun 2020 21:05:56: 2000000 INFO @ Sun, 21 Jun 2020 21:05:58: 7000000 INFO @ Sun, 21 Jun 2020 21:06:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:06:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:06:00: #1 total tags in treatment: 7230463 INFO @ Sun, 21 Jun 2020 21:06:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:06:00: #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 21:06:00: #1 tags after filtering in treatment: 7230414 INFO @ Sun, 21 Jun 2020 21:06:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:06:00: #1 finished! INFO @ Sun, 21 Jun 2020 21:06:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:06:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:06:01: #2 number of paired peaks: 1771 INFO @ Sun, 21 Jun 2020 21:06:01: start model_add_line... INFO @ Sun, 21 Jun 2020 21:06:01: start X-correlation... INFO @ Sun, 21 Jun 2020 21:06:01: end of X-cor INFO @ Sun, 21 Jun 2020 21:06:01: #2 finished! INFO @ Sun, 21 Jun 2020 21:06:01: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 21:06:01: #2 alternative fragment length(s) may be 113 bps INFO @ Sun, 21 Jun 2020 21:06:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.05_model.r INFO @ Sun, 21 Jun 2020 21:06:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:06:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:06:03: 3000000 INFO @ Sun, 21 Jun 2020 21:06:09: 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 21:06:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.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 21:06:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:06:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:06:15: 5000000 INFO @ Sun, 21 Jun 2020 21:06:19: 1000000 INFO @ Sun, 21 Jun 2020 21:06:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:06:22: 6000000 INFO @ Sun, 21 Jun 2020 21:06:26: 2000000 INFO @ Sun, 21 Jun 2020 21:06:29: 7000000 INFO @ Sun, 21 Jun 2020 21:06:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:06:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:06:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.05_summits.bed INFO @ Sun, 21 Jun 2020 21:06:29: Done! pass1 - making usageList (350 chroms): 2 millis pass2 - checking and writing primary data (8896 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:06:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:06:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:06:30: #1 total tags in treatment: 7230463 INFO @ Sun, 21 Jun 2020 21:06:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:06:30: #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 21:06:31: #1 tags after filtering in treatment: 7230414 INFO @ Sun, 21 Jun 2020 21:06:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:06:31: #1 finished! INFO @ Sun, 21 Jun 2020 21:06:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:06:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:06:32: #2 number of paired peaks: 1771 INFO @ Sun, 21 Jun 2020 21:06:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:06:32: start X-correlation... INFO @ Sun, 21 Jun 2020 21:06:32: end of X-cor INFO @ Sun, 21 Jun 2020 21:06:32: #2 finished! INFO @ Sun, 21 Jun 2020 21:06:32: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 21:06:32: #2 alternative fragment length(s) may be 113 bps INFO @ Sun, 21 Jun 2020 21:06:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.10_model.r INFO @ Sun, 21 Jun 2020 21:06:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:06:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:06:33: 3000000 INFO @ Sun, 21 Jun 2020 21:06:39: 4000000 INFO @ Sun, 21 Jun 2020 21:06:45: 5000000 INFO @ Sun, 21 Jun 2020 21:06:50: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:06:52: 6000000 INFO @ Sun, 21 Jun 2020 21:06:58: 7000000 INFO @ Sun, 21 Jun 2020 21:06:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:06:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:06:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.10_summits.bed INFO @ Sun, 21 Jun 2020 21:06:59: Done! pass1 - making usageList (204 chroms): 1 millis pass2 - checking and writing primary data (4787 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:07:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:07:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:07:00: #1 total tags in treatment: 7230463 INFO @ Sun, 21 Jun 2020 21:07:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:07:00: #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 21:07:00: #1 tags after filtering in treatment: 7230414 INFO @ Sun, 21 Jun 2020 21:07:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:07:00: #1 finished! INFO @ Sun, 21 Jun 2020 21:07:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:07:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:07:01: #2 number of paired peaks: 1771 INFO @ Sun, 21 Jun 2020 21:07:01: start model_add_line... INFO @ Sun, 21 Jun 2020 21:07:01: start X-correlation... INFO @ Sun, 21 Jun 2020 21:07:01: end of X-cor INFO @ Sun, 21 Jun 2020 21:07:01: #2 finished! INFO @ Sun, 21 Jun 2020 21:07:01: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 21:07:01: #2 alternative fragment length(s) may be 113 bps INFO @ Sun, 21 Jun 2020 21:07:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.20_model.r INFO @ Sun, 21 Jun 2020 21:07:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:07:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:07:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:07:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:07:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:07:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669019/SRX4669019.20_summits.bed INFO @ Sun, 21 Jun 2020 21:07:28: Done! pass1 - making usageList (110 chroms): 1 millis pass2 - checking and writing primary data (1638 records, 4 fields): 6 millis CompletedMACS2peakCalling