Job ID = 6451998 SRX = ERX1430242 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:38:36 prefetch.2.10.7: 1) Downloading 'ERR1358767'... 2020-06-21T07:38:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:39:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:39:54 prefetch.2.10.7: 'ERR1358767' is valid 2020-06-21T07:39:54 prefetch.2.10.7: 1) 'ERR1358767' was downloaded successfully Read 12300670 spots for ERR1358767/ERR1358767.sra Written 12300670 spots for ERR1358767/ERR1358767.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:46 12300670 reads; of these: 12300670 (100.00%) were unpaired; of these: 637902 (5.19%) aligned 0 times 9492389 (77.17%) aligned exactly 1 time 2170379 (17.64%) aligned >1 times 94.81% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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] 8251885 / 11662768 = 0.7075 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 16:45:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.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 16:45:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:45:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:46:00: 1000000 INFO @ Sun, 21 Jun 2020 16:46:06: 2000000 INFO @ Sun, 21 Jun 2020 16:46:11: 3000000 INFO @ Sun, 21 Jun 2020 16:46:13: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 16:46:13: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 16:46:13: #1 total tags in treatment: 3410883 INFO @ Sun, 21 Jun 2020 16:46:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:46:13: #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 16:46:14: #1 tags after filtering in treatment: 3410816 INFO @ Sun, 21 Jun 2020 16:46:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:46:14: #1 finished! INFO @ Sun, 21 Jun 2020 16:46:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:46:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:46:14: #2 number of paired peaks: 1814 INFO @ Sun, 21 Jun 2020 16:46:14: start model_add_line... INFO @ Sun, 21 Jun 2020 16:46:14: start X-correlation... INFO @ Sun, 21 Jun 2020 16:46:14: end of X-cor INFO @ Sun, 21 Jun 2020 16:46:14: #2 finished! INFO @ Sun, 21 Jun 2020 16:46:14: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 16:46:14: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 16:46:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.05_model.r INFO @ Sun, 21 Jun 2020 16:46:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:46:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:46:23: #3 Call peaks for each chromosome... 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 16:46:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.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 16:46:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:46:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:46:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:46:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:46:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.05_summits.bed INFO @ Sun, 21 Jun 2020 16:46:27: Done! pass1 - making usageList (529 chroms): 1 millis pass2 - checking and writing primary data (3494 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:46:31: 1000000 INFO @ Sun, 21 Jun 2020 16:46:36: 2000000 INFO @ Sun, 21 Jun 2020 16:46:41: 3000000 INFO @ Sun, 21 Jun 2020 16:46:44: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 16:46:44: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 16:46:44: #1 total tags in treatment: 3410883 INFO @ Sun, 21 Jun 2020 16:46:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:46:44: #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 16:46:44: #1 tags after filtering in treatment: 3410816 INFO @ Sun, 21 Jun 2020 16:46:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:46:44: #1 finished! INFO @ Sun, 21 Jun 2020 16:46:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:46:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:46:44: #2 number of paired peaks: 1814 INFO @ Sun, 21 Jun 2020 16:46:44: start model_add_line... INFO @ Sun, 21 Jun 2020 16:46:44: start X-correlation... INFO @ Sun, 21 Jun 2020 16:46:44: end of X-cor INFO @ Sun, 21 Jun 2020 16:46:44: #2 finished! INFO @ Sun, 21 Jun 2020 16:46:44: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 16:46:44: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 16:46:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.10_model.r INFO @ Sun, 21 Jun 2020 16:46:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:46:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:46:53: #3 Call peaks for each chromosome... 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 16:46:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.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 16:46:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:46:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:46:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:46:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:46:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.10_summits.bed INFO @ Sun, 21 Jun 2020 16:46:57: Done! pass1 - making usageList (274 chroms): 1 millis pass2 - checking and writing primary data (1700 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:47:01: 1000000 INFO @ Sun, 21 Jun 2020 16:47:06: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:47:11: 3000000 INFO @ Sun, 21 Jun 2020 16:47:14: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 16:47:14: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 16:47:14: #1 total tags in treatment: 3410883 INFO @ Sun, 21 Jun 2020 16:47:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:47:14: #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 16:47:14: #1 tags after filtering in treatment: 3410816 INFO @ Sun, 21 Jun 2020 16:47:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:47:14: #1 finished! INFO @ Sun, 21 Jun 2020 16:47:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:47:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:47:14: #2 number of paired peaks: 1814 INFO @ Sun, 21 Jun 2020 16:47:14: start model_add_line... INFO @ Sun, 21 Jun 2020 16:47:14: start X-correlation... INFO @ Sun, 21 Jun 2020 16:47:14: end of X-cor INFO @ Sun, 21 Jun 2020 16:47:14: #2 finished! INFO @ Sun, 21 Jun 2020 16:47:14: #2 predicted fragment length is 134 bps INFO @ Sun, 21 Jun 2020 16:47:14: #2 alternative fragment length(s) may be 134 bps INFO @ Sun, 21 Jun 2020 16:47:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.20_model.r INFO @ Sun, 21 Jun 2020 16:47:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:47:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:47:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:47:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:47:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:47:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX1430242/ERX1430242.20_summits.bed INFO @ Sun, 21 Jun 2020 16:47:27: Done! pass1 - making usageList (158 chroms): 1 millis pass2 - checking and writing primary data (721 records, 4 fields): 7 millis CompletedMACS2peakCalling