Job ID = 6456247 SRX = SRX331400 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:34:11 prefetch.2.10.7: 1) Downloading 'SRR947637'... 2020-06-21T10:34:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:39:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:39:28 prefetch.2.10.7: 1) 'SRR947637' was downloaded successfully Read 17286773 spots for SRR947637/SRR947637.sra Written 17286773 spots for SRR947637/SRR947637.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: 00:04:00 17286773 reads; of these: 17286773 (100.00%) were unpaired; of these: 1674183 (9.68%) aligned 0 times 13278410 (76.81%) aligned exactly 1 time 2334180 (13.50%) aligned >1 times 90.32% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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] 4707196 / 15612590 = 0.3015 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 19:48:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.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 19:48:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:32: 1000000 INFO @ Sun, 21 Jun 2020 19:48:37: 2000000 INFO @ Sun, 21 Jun 2020 19:48:43: 3000000 INFO @ Sun, 21 Jun 2020 19:48:48: 4000000 INFO @ Sun, 21 Jun 2020 19:48:53: 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 19:48:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.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 19:48:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:59: 6000000 INFO @ Sun, 21 Jun 2020 19:49:03: 1000000 INFO @ Sun, 21 Jun 2020 19:49:05: 7000000 INFO @ Sun, 21 Jun 2020 19:49:09: 2000000 INFO @ Sun, 21 Jun 2020 19:49:11: 8000000 INFO @ Sun, 21 Jun 2020 19:49:14: 3000000 INFO @ Sun, 21 Jun 2020 19:49:17: 9000000 INFO @ Sun, 21 Jun 2020 19:49:21: 4000000 INFO @ Sun, 21 Jun 2020 19:49:23: 10000000 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 19:49:26: 5000000 INFO @ Sun, 21 Jun 2020 19:49:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.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 19:49:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:49:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:49:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:49:29: #1 total tags in treatment: 10905394 INFO @ Sun, 21 Jun 2020 19:49:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:49:29: #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 19:49:29: #1 tags after filtering in treatment: 10905380 INFO @ Sun, 21 Jun 2020 19:49:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:49:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:49:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:49:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:49:31: #2 number of paired peaks: 5076 INFO @ Sun, 21 Jun 2020 19:49:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:49:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:49:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:49:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:49:31: #2 predicted fragment length is 233 bps INFO @ Sun, 21 Jun 2020 19:49:31: #2 alternative fragment length(s) may be 233 bps INFO @ Sun, 21 Jun 2020 19:49:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.05_model.r INFO @ Sun, 21 Jun 2020 19:49:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:49:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:49:33: 6000000 INFO @ Sun, 21 Jun 2020 19:49:33: 1000000 INFO @ Sun, 21 Jun 2020 19:49:39: 7000000 INFO @ Sun, 21 Jun 2020 19:49:39: 2000000 INFO @ Sun, 21 Jun 2020 19:49:45: 8000000 INFO @ Sun, 21 Jun 2020 19:49:45: 3000000 INFO @ Sun, 21 Jun 2020 19:49:51: 9000000 INFO @ Sun, 21 Jun 2020 19:49:51: 4000000 INFO @ Sun, 21 Jun 2020 19:49:57: 5000000 INFO @ Sun, 21 Jun 2020 19:49:57: 10000000 INFO @ Sun, 21 Jun 2020 19:50:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:50:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:50:03: #1 total tags in treatment: 10905394 INFO @ Sun, 21 Jun 2020 19:50:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:03: #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 19:50:03: 6000000 INFO @ Sun, 21 Jun 2020 19:50:03: #1 tags after filtering in treatment: 10905380 INFO @ Sun, 21 Jun 2020 19:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:50:05: #2 number of paired peaks: 5076 INFO @ Sun, 21 Jun 2020 19:50:05: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:05: #2 predicted fragment length is 233 bps INFO @ Sun, 21 Jun 2020 19:50:05: #2 alternative fragment length(s) may be 233 bps INFO @ Sun, 21 Jun 2020 19:50:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.10_model.r INFO @ Sun, 21 Jun 2020 19:50:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:09: 7000000 INFO @ Sun, 21 Jun 2020 19:50:15: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:50:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.05_summits.bed INFO @ Sun, 21 Jun 2020 19:50:18: Done! pass1 - making usageList (477 chroms): 2 millis pass2 - checking and writing primary data (8160 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:50:21: 9000000 INFO @ Sun, 21 Jun 2020 19:50:27: 10000000 INFO @ Sun, 21 Jun 2020 19:50:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:50:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:50:32: #1 total tags in treatment: 10905394 INFO @ Sun, 21 Jun 2020 19:50:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:32: #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 19:50:32: #1 tags after filtering in treatment: 10905380 INFO @ Sun, 21 Jun 2020 19:50:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:34: #2 number of paired peaks: 5076 INFO @ Sun, 21 Jun 2020 19:50:34: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:34: #2 predicted fragment length is 233 bps INFO @ Sun, 21 Jun 2020 19:50:34: #2 alternative fragment length(s) may be 233 bps INFO @ Sun, 21 Jun 2020 19:50:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.20_model.r INFO @ Sun, 21 Jun 2020 19:50:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:50:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.10_summits.bed INFO @ Sun, 21 Jun 2020 19:50:49: Done! pass1 - making usageList (422 chroms): 2 millis pass2 - checking and writing primary data (6791 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:51:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331400/SRX331400.20_summits.bed INFO @ Sun, 21 Jun 2020 19:51:20: Done! pass1 - making usageList (318 chroms): 2 millis pass2 - checking and writing primary data (5263 records, 4 fields): 14 millis CompletedMACS2peakCalling