Job ID = 6452282 SRX = ERX3548053 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:27:35 prefetch.2.10.7: 1) Downloading 'ERR3528415'... 2020-06-21T07:27:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:28:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:28:19 prefetch.2.10.7: 'ERR3528415' is valid 2020-06-21T07:28:19 prefetch.2.10.7: 1) 'ERR3528415' was downloaded successfully Read 3686944 spots for ERR3528415/ERR3528415.sra Written 3686944 spots for ERR3528415/ERR3528415.sra 2020-06-21T07:28:47 prefetch.2.10.7: 1) Downloading 'ERR3528416'... 2020-06-21T07:28:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:29:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:29:33 prefetch.2.10.7: 'ERR3528416' is valid 2020-06-21T07:29:33 prefetch.2.10.7: 1) 'ERR3528416' was downloaded successfully Read 3653503 spots for ERR3528416/ERR3528416.sra Written 3653503 spots for ERR3528416/ERR3528416.sra 2020-06-21T07:30:01 prefetch.2.10.7: 1) Downloading 'ERR3528417'... 2020-06-21T07:30:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:31:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:31:19 prefetch.2.10.7: 'ERR3528417' is valid 2020-06-21T07:31:19 prefetch.2.10.7: 1) 'ERR3528417' was downloaded successfully Read 3706979 spots for ERR3528417/ERR3528417.sra Written 3706979 spots for ERR3528417/ERR3528417.sra 2020-06-21T07:31:47 prefetch.2.10.7: 1) Downloading 'ERR3528418'... 2020-06-21T07:31:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:32:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:32:28 prefetch.2.10.7: 'ERR3528418' is valid 2020-06-21T07:32:28 prefetch.2.10.7: 1) 'ERR3528418' was downloaded successfully Read 3632397 spots for ERR3528418/ERR3528418.sra Written 3632397 spots for ERR3528418/ERR3528418.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: 00:03:22 14679823 reads; of these: 14679823 (100.00%) were unpaired; of these: 2275984 (15.50%) aligned 0 times 9445795 (64.35%) aligned exactly 1 time 2958044 (20.15%) aligned >1 times 84.50% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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] 7593641 / 12403839 = 0.6122 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 16:39:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.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 16:39:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:39:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:39:16: 1000000 INFO @ Sun, 21 Jun 2020 16:39:21: 2000000 INFO @ Sun, 21 Jun 2020 16:39:26: 3000000 INFO @ Sun, 21 Jun 2020 16:39:32: 4000000 INFO @ Sun, 21 Jun 2020 16:39:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 16:39:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 16:39:36: #1 total tags in treatment: 4810198 INFO @ Sun, 21 Jun 2020 16:39:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:39:36: #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 16:39:37: #1 tags after filtering in treatment: 4810083 INFO @ Sun, 21 Jun 2020 16:39:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:39:37: #1 finished! INFO @ Sun, 21 Jun 2020 16:39:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:39:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:39:38: #2 number of paired peaks: 5795 INFO @ Sun, 21 Jun 2020 16:39:38: start model_add_line... INFO @ Sun, 21 Jun 2020 16:39:38: start X-correlation... INFO @ Sun, 21 Jun 2020 16:39:38: end of X-cor INFO @ Sun, 21 Jun 2020 16:39:38: #2 finished! INFO @ Sun, 21 Jun 2020 16:39:38: #2 predicted fragment length is 244 bps INFO @ Sun, 21 Jun 2020 16:39:38: #2 alternative fragment length(s) may be 244 bps INFO @ Sun, 21 Jun 2020 16:39:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.05_model.r INFO @ Sun, 21 Jun 2020 16:39:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:39:38: #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 16:39:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.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 16:39:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:39:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:39:46: 1000000 INFO @ Sun, 21 Jun 2020 16:39:51: 2000000 INFO @ Sun, 21 Jun 2020 16:39:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:39:56: 3000000 INFO @ Sun, 21 Jun 2020 16:39:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:39:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:39:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.05_summits.bed INFO @ Sun, 21 Jun 2020 16:39:58: Done! pass1 - making usageList (573 chroms): 2 millis pass2 - checking and writing primary data (6828 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:40:02: 4000000 INFO @ Sun, 21 Jun 2020 16:40:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 16:40:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 16:40:06: #1 total tags in treatment: 4810198 INFO @ Sun, 21 Jun 2020 16:40:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:40:06: #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 16:40:07: #1 tags after filtering in treatment: 4810083 INFO @ Sun, 21 Jun 2020 16:40:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:40:07: #1 finished! INFO @ Sun, 21 Jun 2020 16:40:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:40:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:40:07: #2 number of paired peaks: 5795 INFO @ Sun, 21 Jun 2020 16:40:07: start model_add_line... INFO @ Sun, 21 Jun 2020 16:40:08: start X-correlation... INFO @ Sun, 21 Jun 2020 16:40:08: end of X-cor INFO @ Sun, 21 Jun 2020 16:40:08: #2 finished! INFO @ Sun, 21 Jun 2020 16:40:08: #2 predicted fragment length is 244 bps INFO @ Sun, 21 Jun 2020 16:40:08: #2 alternative fragment length(s) may be 244 bps INFO @ Sun, 21 Jun 2020 16:40:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.10_model.r INFO @ Sun, 21 Jun 2020 16:40:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:40:08: #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 16:40:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.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 16:40:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:40:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:40:16: 1000000 INFO @ Sun, 21 Jun 2020 16:40:21: 2000000 INFO @ Sun, 21 Jun 2020 16:40:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:40:26: 3000000 INFO @ Sun, 21 Jun 2020 16:40:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:40:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:40:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.10_summits.bed INFO @ Sun, 21 Jun 2020 16:40:27: Done! pass1 - making usageList (490 chroms): 1 millis pass2 - checking and writing primary data (5106 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:40:32: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:40:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 16:40:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 16:40:37: #1 total tags in treatment: 4810198 INFO @ Sun, 21 Jun 2020 16:40:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:40:37: #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 16:40:37: #1 tags after filtering in treatment: 4810083 INFO @ Sun, 21 Jun 2020 16:40:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:40:37: #1 finished! INFO @ Sun, 21 Jun 2020 16:40:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:40:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:40:38: #2 number of paired peaks: 5795 INFO @ Sun, 21 Jun 2020 16:40:38: start model_add_line... INFO @ Sun, 21 Jun 2020 16:40:38: start X-correlation... INFO @ Sun, 21 Jun 2020 16:40:38: end of X-cor INFO @ Sun, 21 Jun 2020 16:40:38: #2 finished! INFO @ Sun, 21 Jun 2020 16:40:38: #2 predicted fragment length is 244 bps INFO @ Sun, 21 Jun 2020 16:40:38: #2 alternative fragment length(s) may be 244 bps INFO @ Sun, 21 Jun 2020 16:40:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.20_model.r INFO @ Sun, 21 Jun 2020 16:40:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:40:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:40:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:40:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:40:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:40:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX3548053/ERX3548053.20_summits.bed INFO @ Sun, 21 Jun 2020 16:40:58: Done! pass1 - making usageList (328 chroms): 2 millis pass2 - checking and writing primary data (3205 records, 4 fields): 22 millis CompletedMACS2peakCalling