Job ID = 6453880 SRX = SRX1550614 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:42:17 prefetch.2.10.7: 1) Downloading 'SRR3130875'... 2020-06-21T08:42:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:43:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:43:12 prefetch.2.10.7: 'SRR3130875' is valid 2020-06-21T08:43:12 prefetch.2.10.7: 1) 'SRR3130875' was downloaded successfully Read 4000000 spots for SRR3130875/SRR3130875.sra Written 4000000 spots for SRR3130875/SRR3130875.sra 2020-06-21T08:43:34 prefetch.2.10.7: 1) Downloading 'SRR3130876'... 2020-06-21T08:43:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:43:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:43:58 prefetch.2.10.7: 'SRR3130876' is valid 2020-06-21T08:43:58 prefetch.2.10.7: 1) 'SRR3130876' was downloaded successfully Read 549698 spots for SRR3130876/SRR3130876.sra Written 549698 spots for SRR3130876/SRR3130876.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: 00:01:04 4549698 reads; of these: 4549698 (100.00%) were unpaired; of these: 583662 (12.83%) aligned 0 times 3469745 (76.26%) aligned exactly 1 time 496291 (10.91%) aligned >1 times 87.17% overall alignment rate Time searching: 00:01:04 Overall time: 00:01:04 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] 589427 / 3966036 = 0.1486 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 17:46:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.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 17:46:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:46:44: 1000000 INFO @ Sun, 21 Jun 2020 17:46:50: 2000000 INFO @ Sun, 21 Jun 2020 17:46:57: 3000000 INFO @ Sun, 21 Jun 2020 17:47:00: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:47:00: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:47:00: #1 total tags in treatment: 3376609 INFO @ Sun, 21 Jun 2020 17:47:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:47:00: #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 17:47:00: #1 tags after filtering in treatment: 3376459 INFO @ Sun, 21 Jun 2020 17:47:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:00: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:47:00: #2 number of paired peaks: 4966 INFO @ Sun, 21 Jun 2020 17:47:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:47:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:47:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:47:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:47:00: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 17:47:00: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 17:47:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.05_model.r INFO @ Sun, 21 Jun 2020 17:47:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:47:00: #3 Pre-compute pvalue-qvalue table... 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 17:47:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.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 17:47:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:47:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.05_summits.bed INFO @ Sun, 21 Jun 2020 17:47:14: Done! pass1 - making usageList (220 chroms): 2 millis pass2 - checking and writing primary data (6870 records, 4 fields): 18 millis INFO @ Sun, 21 Jun 2020 17:47:14: 1000000 CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:47:20: 2000000 INFO @ Sun, 21 Jun 2020 17:47:27: 3000000 INFO @ Sun, 21 Jun 2020 17:47:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:47:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:47:29: #1 total tags in treatment: 3376609 INFO @ Sun, 21 Jun 2020 17:47:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:47:29: #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 17:47:29: #1 tags after filtering in treatment: 3376459 INFO @ Sun, 21 Jun 2020 17:47:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:29: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:47:30: #2 number of paired peaks: 4966 INFO @ Sun, 21 Jun 2020 17:47:30: start model_add_line... INFO @ Sun, 21 Jun 2020 17:47:30: start X-correlation... INFO @ Sun, 21 Jun 2020 17:47:30: end of X-cor INFO @ Sun, 21 Jun 2020 17:47:30: #2 finished! INFO @ Sun, 21 Jun 2020 17:47:30: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 17:47:30: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 17:47:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.10_model.r INFO @ Sun, 21 Jun 2020 17:47:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:47:30: #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 17:47:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.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 17:47:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:47:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.10_summits.bed INFO @ Sun, 21 Jun 2020 17:47:43: Done! pass1 - making usageList (118 chroms): 1 millis pass2 - checking and writing primary data (4455 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:47:44: 1000000 INFO @ Sun, 21 Jun 2020 17:47:50: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:47:56: 3000000 INFO @ Sun, 21 Jun 2020 17:47:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:47:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:47:59: #1 total tags in treatment: 3376609 INFO @ Sun, 21 Jun 2020 17:47:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:47:59: #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 17:47:59: #1 tags after filtering in treatment: 3376459 INFO @ Sun, 21 Jun 2020 17:47:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:59: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:00: #2 number of paired peaks: 4966 INFO @ Sun, 21 Jun 2020 17:48:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:00: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 17:48:00: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 17:48:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.20_model.r INFO @ Sun, 21 Jun 2020 17:48:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:48:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:48:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:48:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:48:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550614/SRX1550614.20_summits.bed INFO @ Sun, 21 Jun 2020 17:48:13: Done! pass1 - making usageList (71 chroms): 1 millis pass2 - checking and writing primary data (2779 records, 4 fields): 6 millis CompletedMACS2peakCalling