Job ID = 6459238 SRX = SRX6468484 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:12:35 prefetch.2.10.7: 1) Downloading 'SRR9710570'... 2020-06-21T13:12:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:18:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:18:39 prefetch.2.10.7: 1) 'SRR9710570' was downloaded successfully Read 30617151 spots for SRR9710570/SRR9710570.sra Written 30617151 spots for SRR9710570/SRR9710570.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: 00:06:45 30617151 reads; of these: 30617151 (100.00%) were unpaired; of these: 5086700 (16.61%) aligned 0 times 20966000 (68.48%) aligned exactly 1 time 4564451 (14.91%) aligned >1 times 83.39% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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 12 files... [bam_rmdupse_core] 16134037 / 25530451 = 0.6320 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 22:33:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.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 22:33:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:33:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:33:29: 1000000 INFO @ Sun, 21 Jun 2020 22:33:34: 2000000 INFO @ Sun, 21 Jun 2020 22:33:39: 3000000 INFO @ Sun, 21 Jun 2020 22:33:44: 4000000 INFO @ Sun, 21 Jun 2020 22:33:50: 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 22:33:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.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 22:33:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:33:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:33:55: 6000000 INFO @ Sun, 21 Jun 2020 22:33:59: 1000000 INFO @ Sun, 21 Jun 2020 22:34:01: 7000000 INFO @ Sun, 21 Jun 2020 22:34:05: 2000000 INFO @ Sun, 21 Jun 2020 22:34:08: 8000000 INFO @ Sun, 21 Jun 2020 22:34:10: 3000000 INFO @ Sun, 21 Jun 2020 22:34:13: 9000000 INFO @ Sun, 21 Jun 2020 22:34:16: 4000000 INFO @ Sun, 21 Jun 2020 22:34:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:34:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:34:16: #1 total tags in treatment: 9396414 INFO @ Sun, 21 Jun 2020 22:34:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:34:16: #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 22:34:17: #1 tags after filtering in treatment: 9396411 INFO @ Sun, 21 Jun 2020 22:34:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:34:17: #1 finished! INFO @ Sun, 21 Jun 2020 22:34:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:34:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:34:18: #2 number of paired peaks: 2374 INFO @ Sun, 21 Jun 2020 22:34:18: start model_add_line... INFO @ Sun, 21 Jun 2020 22:34:18: start X-correlation... INFO @ Sun, 21 Jun 2020 22:34:18: end of X-cor INFO @ Sun, 21 Jun 2020 22:34:18: #2 finished! INFO @ Sun, 21 Jun 2020 22:34:18: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 22:34:18: #2 alternative fragment length(s) may be 4,155 bps INFO @ Sun, 21 Jun 2020 22:34:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.05_model.r INFO @ Sun, 21 Jun 2020 22:34:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:34:18: #3 Pre-compute pvalue-qvalue table... 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 22:34:21: 5000000 INFO @ Sun, 21 Jun 2020 22:34:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.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 22:34:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:34:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:34:27: 6000000 INFO @ Sun, 21 Jun 2020 22:34:29: 1000000 INFO @ Sun, 21 Jun 2020 22:34:33: 7000000 INFO @ Sun, 21 Jun 2020 22:34:35: 2000000 INFO @ Sun, 21 Jun 2020 22:34:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:34:39: 8000000 INFO @ Sun, 21 Jun 2020 22:34:41: 3000000 INFO @ Sun, 21 Jun 2020 22:34:45: 9000000 INFO @ Sun, 21 Jun 2020 22:34:47: 4000000 INFO @ Sun, 21 Jun 2020 22:34:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:34:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:34:48: #1 total tags in treatment: 9396414 INFO @ Sun, 21 Jun 2020 22:34:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:34:48: #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 22:34:48: #1 tags after filtering in treatment: 9396411 INFO @ Sun, 21 Jun 2020 22:34:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:34:48: #1 finished! INFO @ Sun, 21 Jun 2020 22:34:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:34:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:34:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:34:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:34:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.05_summits.bed INFO @ Sun, 21 Jun 2020 22:34:49: Done! INFO @ Sun, 21 Jun 2020 22:34:49: #2 number of paired peaks: 2374 INFO @ Sun, 21 Jun 2020 22:34:49: start model_add_line... pass1 - making usageList (541 chroms): 2 millis INFO @ Sun, 21 Jun 2020 22:34:49: start X-correlation... INFO @ Sun, 21 Jun 2020 22:34:50: end of X-cor INFO @ Sun, 21 Jun 2020 22:34:50: #2 finished! INFO @ Sun, 21 Jun 2020 22:34:50: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 22:34:50: #2 alternative fragment length(s) may be 4,155 bps INFO @ Sun, 21 Jun 2020 22:34:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.10_model.r INFO @ Sun, 21 Jun 2020 22:34:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:34:50: #3 Pre-compute pvalue-qvalue table... pass2 - checking and writing primary data (7020 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:34:53: 5000000 INFO @ Sun, 21 Jun 2020 22:34:58: 6000000 INFO @ Sun, 21 Jun 2020 22:35:03: 7000000 INFO @ Sun, 21 Jun 2020 22:35:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:35:10: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:35:15: 9000000 INFO @ Sun, 21 Jun 2020 22:35:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:35:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:35:18: #1 total tags in treatment: 9396414 INFO @ Sun, 21 Jun 2020 22:35:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:35:18: #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 22:35:19: #1 tags after filtering in treatment: 9396411 INFO @ Sun, 21 Jun 2020 22:35:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:35:19: #1 finished! INFO @ Sun, 21 Jun 2020 22:35:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:35:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:35:19: #2 number of paired peaks: 2374 INFO @ Sun, 21 Jun 2020 22:35:19: start model_add_line... INFO @ Sun, 21 Jun 2020 22:35:20: start X-correlation... INFO @ Sun, 21 Jun 2020 22:35:20: end of X-cor INFO @ Sun, 21 Jun 2020 22:35:20: #2 finished! INFO @ Sun, 21 Jun 2020 22:35:20: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 22:35:20: #2 alternative fragment length(s) may be 4,155 bps INFO @ Sun, 21 Jun 2020 22:35:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.20_model.r INFO @ Sun, 21 Jun 2020 22:35:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:35:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.10_summits.bed INFO @ Sun, 21 Jun 2020 22:35:20: Done! pass1 - making usageList (449 chroms): 2 millis pass2 - checking and writing primary data (5495 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:35:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:35:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:35:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:35:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468484/SRX6468484.20_summits.bed INFO @ Sun, 21 Jun 2020 22:35:49: Done! pass1 - making usageList (388 chroms): 2 millis pass2 - checking and writing primary data (3095 records, 4 fields): 24 millis CompletedMACS2peakCalling