Job ID = 6452000 SRX = ERX1430244 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:40:51 prefetch.2.10.7: 1) Downloading 'ERR1358769'... 2020-06-21T07:40:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:44:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:44:51 prefetch.2.10.7: 'ERR1358769' is valid 2020-06-21T07:44:51 prefetch.2.10.7: 1) 'ERR1358769' was downloaded successfully Read 13476376 spots for ERR1358769/ERR1358769.sra Written 13476376 spots for ERR1358769/ERR1358769.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: 00:03:30 13476376 reads; of these: 13476376 (100.00%) were unpaired; of these: 720004 (5.34%) aligned 0 times 9510144 (70.57%) aligned exactly 1 time 3246228 (24.09%) aligned >1 times 94.66% overall alignment rate Time searching: 00:03:31 Overall time: 00:03:31 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] 9071223 / 12756372 = 0.7111 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 16:51:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.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 16:51:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:51:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:51:39: 1000000 INFO @ Sun, 21 Jun 2020 16:51:46: 2000000 INFO @ Sun, 21 Jun 2020 16:51:52: 3000000 INFO @ Sun, 21 Jun 2020 16:51:57: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 16:51:57: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 16:51:57: #1 total tags in treatment: 3685149 INFO @ Sun, 21 Jun 2020 16:51:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:51:57: #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 16:51:57: #1 tags after filtering in treatment: 3685131 INFO @ Sun, 21 Jun 2020 16:51:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:51:57: #1 finished! INFO @ Sun, 21 Jun 2020 16:51:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:51:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:51:58: #2 number of paired peaks: 1840 INFO @ Sun, 21 Jun 2020 16:51:58: start model_add_line... INFO @ Sun, 21 Jun 2020 16:51:58: start X-correlation... INFO @ Sun, 21 Jun 2020 16:51:58: end of X-cor INFO @ Sun, 21 Jun 2020 16:51:58: #2 finished! INFO @ Sun, 21 Jun 2020 16:51:58: #2 predicted fragment length is 89 bps INFO @ Sun, 21 Jun 2020 16:51:58: #2 alternative fragment length(s) may be 89 bps INFO @ Sun, 21 Jun 2020 16:51:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.05_model.r INFO @ Sun, 21 Jun 2020 16:51:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:51:58: #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 16:52:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.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 16:52:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:52:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:52:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:52:09: 1000000 INFO @ Sun, 21 Jun 2020 16:52:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:52:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:52:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.05_summits.bed INFO @ Sun, 21 Jun 2020 16:52:10: Done! pass1 - making usageList (673 chroms): 1 millis pass2 - checking and writing primary data (2721 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:52:16: 2000000 INFO @ Sun, 21 Jun 2020 16:52:23: 3000000 INFO @ Sun, 21 Jun 2020 16:52:27: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 16:52:27: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 16:52:27: #1 total tags in treatment: 3685149 INFO @ Sun, 21 Jun 2020 16:52:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:52:27: #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 16:52:28: #1 tags after filtering in treatment: 3685131 INFO @ Sun, 21 Jun 2020 16:52:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:52:28: #1 finished! INFO @ Sun, 21 Jun 2020 16:52:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:52:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:52:28: #2 number of paired peaks: 1840 INFO @ Sun, 21 Jun 2020 16:52:28: start model_add_line... INFO @ Sun, 21 Jun 2020 16:52:28: start X-correlation... INFO @ Sun, 21 Jun 2020 16:52:28: end of X-cor INFO @ Sun, 21 Jun 2020 16:52:28: #2 finished! INFO @ Sun, 21 Jun 2020 16:52:28: #2 predicted fragment length is 89 bps INFO @ Sun, 21 Jun 2020 16:52:28: #2 alternative fragment length(s) may be 89 bps INFO @ Sun, 21 Jun 2020 16:52:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.10_model.r INFO @ Sun, 21 Jun 2020 16:52:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:52:28: #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 16:52:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.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 16:52:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:52:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:52:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:52:39: 1000000 INFO @ Sun, 21 Jun 2020 16:52:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:52:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:52:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.10_summits.bed INFO @ Sun, 21 Jun 2020 16:52:41: Done! pass1 - making usageList (544 chroms): 1 millis pass2 - checking and writing primary data (1743 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:52:46: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:52:53: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:52:58: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 16:52:58: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 16:52:58: #1 total tags in treatment: 3685149 INFO @ Sun, 21 Jun 2020 16:52:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:52:58: #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 16:52:58: #1 tags after filtering in treatment: 3685131 INFO @ Sun, 21 Jun 2020 16:52:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:52:58: #1 finished! INFO @ Sun, 21 Jun 2020 16:52:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:52:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:52:59: #2 number of paired peaks: 1840 INFO @ Sun, 21 Jun 2020 16:52:59: start model_add_line... INFO @ Sun, 21 Jun 2020 16:52:59: start X-correlation... INFO @ Sun, 21 Jun 2020 16:52:59: end of X-cor INFO @ Sun, 21 Jun 2020 16:52:59: #2 finished! INFO @ Sun, 21 Jun 2020 16:52:59: #2 predicted fragment length is 89 bps INFO @ Sun, 21 Jun 2020 16:52:59: #2 alternative fragment length(s) may be 89 bps INFO @ Sun, 21 Jun 2020 16:52:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.20_model.r INFO @ Sun, 21 Jun 2020 16:52:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:52:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:53:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:53:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:53:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX1430244/ERX1430244.20_summits.bed INFO @ Sun, 21 Jun 2020 16:53:12: Done! pass1 - making usageList (356 chroms): 1 millis pass2 - checking and writing primary data (848 records, 4 fields): 12 millis CompletedMACS2peakCalling