Job ID = 6452449 SRX = SRX013068 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:04:38 prefetch.2.10.7: 1) Downloading 'SRR030334'... 2020-06-21T08:04:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:06:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:06:44 prefetch.2.10.7: 'SRR030334' is valid 2020-06-21T08:06:44 prefetch.2.10.7: 1) 'SRR030334' was downloaded successfully Read 8605233 spots for SRR030334/SRR030334.sra Written 8605233 spots for SRR030334/SRR030334.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: 00:01:21 8605233 reads; of these: 8605233 (100.00%) were unpaired; of these: 505128 (5.87%) aligned 0 times 7404122 (86.04%) aligned exactly 1 time 695983 (8.09%) aligned >1 times 94.13% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 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] 2127255 / 8100105 = 0.2626 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 17:10:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.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 17:10:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:10:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:10:34: 1000000 INFO @ Sun, 21 Jun 2020 17:10:39: 2000000 INFO @ Sun, 21 Jun 2020 17:10:43: 3000000 INFO @ Sun, 21 Jun 2020 17:10:48: 4000000 INFO @ Sun, 21 Jun 2020 17:10:53: 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 17:10:58: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:10:58: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:10:58: #1 total tags in treatment: 5972850 INFO @ Sun, 21 Jun 2020 17:10:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:10:58: #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 17:10:58: #1 tags after filtering in treatment: 5972678 INFO @ Sun, 21 Jun 2020 17:10:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:10:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:10:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:10:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:10:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.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 17:10:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:10:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:10:59: #2 number of paired peaks: 8759 INFO @ Sun, 21 Jun 2020 17:10:59: start model_add_line... INFO @ Sun, 21 Jun 2020 17:10:59: start X-correlation... INFO @ Sun, 21 Jun 2020 17:10:59: end of X-cor INFO @ Sun, 21 Jun 2020 17:10:59: #2 finished! INFO @ Sun, 21 Jun 2020 17:10:59: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 17:10:59: #2 alternative fragment length(s) may be 101 bps INFO @ Sun, 21 Jun 2020 17:10:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.05_model.r INFO @ Sun, 21 Jun 2020 17:10:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:10:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:11:04: 1000000 INFO @ Sun, 21 Jun 2020 17:11:08: 2000000 INFO @ Sun, 21 Jun 2020 17:11:13: 3000000 INFO @ Sun, 21 Jun 2020 17:11:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:11:18: 4000000 INFO @ Sun, 21 Jun 2020 17:11:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:11:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:11:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.05_summits.bed INFO @ Sun, 21 Jun 2020 17:11:23: Done! INFO @ Sun, 21 Jun 2020 17:11:23: 5000000 pass1 - making usageList (87 chroms): 2 millis pass2 - checking and writing primary data (7746 records, 4 fields): 11 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 17:11:28: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:11:28: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:11:28: #1 total tags in treatment: 5972850 INFO @ Sun, 21 Jun 2020 17:11:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:11:28: #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 17:11:28: #1 tags after filtering in treatment: 5972678 INFO @ Sun, 21 Jun 2020 17:11:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:11:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:11:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:11:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:11:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.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 17:11:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:11:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:11:29: #2 number of paired peaks: 8759 INFO @ Sun, 21 Jun 2020 17:11:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:11:30: start X-correlation... INFO @ Sun, 21 Jun 2020 17:11:30: end of X-cor INFO @ Sun, 21 Jun 2020 17:11:30: #2 finished! INFO @ Sun, 21 Jun 2020 17:11:30: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 17:11:30: #2 alternative fragment length(s) may be 101 bps INFO @ Sun, 21 Jun 2020 17:11:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.10_model.r INFO @ Sun, 21 Jun 2020 17:11:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:11:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:11:34: 1000000 INFO @ Sun, 21 Jun 2020 17:11:39: 2000000 INFO @ Sun, 21 Jun 2020 17:11:44: 3000000 INFO @ Sun, 21 Jun 2020 17:11:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:11:49: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:11:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:11:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:11:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.10_summits.bed INFO @ Sun, 21 Jun 2020 17:11:53: Done! pass1 - making usageList (59 chroms): 1 millis pass2 - checking and writing primary data (6938 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:11:54: 5000000 INFO @ Sun, 21 Jun 2020 17:11:59: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:11:59: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:11:59: #1 total tags in treatment: 5972850 INFO @ Sun, 21 Jun 2020 17:11:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:11:59: #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 17:11:59: #1 tags after filtering in treatment: 5972678 INFO @ Sun, 21 Jun 2020 17:11:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:11:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:11:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:11:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:12:00: #2 number of paired peaks: 8759 INFO @ Sun, 21 Jun 2020 17:12:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:12:01: start X-correlation... INFO @ Sun, 21 Jun 2020 17:12:01: end of X-cor INFO @ Sun, 21 Jun 2020 17:12:01: #2 finished! INFO @ Sun, 21 Jun 2020 17:12:01: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 17:12:01: #2 alternative fragment length(s) may be 101 bps INFO @ Sun, 21 Jun 2020 17:12:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.20_model.r INFO @ Sun, 21 Jun 2020 17:12:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:12:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:12:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:12:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:12:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:12:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013068/SRX013068.20_summits.bed INFO @ Sun, 21 Jun 2020 17:12:24: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (5785 records, 4 fields): 7 millis CompletedMACS2peakCalling