Job ID = 6452413 SRX = SRX013042 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:57:15 prefetch.2.10.7: 1) Downloading 'SRR030308'... 2020-06-21T07:57:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:58:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:58:46 prefetch.2.10.7: 'SRR030308' is valid 2020-06-21T07:58:46 prefetch.2.10.7: 1) 'SRR030308' was downloaded successfully Read 5063524 spots for SRR030308/SRR030308.sra Written 5063524 spots for SRR030308/SRR030308.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: 00:00:46 5063524 reads; of these: 5063524 (100.00%) were unpaired; of these: 814991 (16.10%) aligned 0 times 3899826 (77.02%) aligned exactly 1 time 348707 (6.89%) aligned >1 times 83.90% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 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] 287523 / 4248533 = 0.0677 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 17:01:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.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 17:01:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:01:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:01:40: 1000000 INFO @ Sun, 21 Jun 2020 17:01:46: 2000000 INFO @ Sun, 21 Jun 2020 17:01:51: 3000000 INFO @ Sun, 21 Jun 2020 17:01:57: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:01:57: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:01:57: #1 total tags in treatment: 3961010 INFO @ Sun, 21 Jun 2020 17:01:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:01:57: #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 17:01:58: #1 tags after filtering in treatment: 3960631 INFO @ Sun, 21 Jun 2020 17:01:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:01:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:01:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:01:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:01:58: #2 number of paired peaks: 1993 INFO @ Sun, 21 Jun 2020 17:01:58: start model_add_line... INFO @ Sun, 21 Jun 2020 17:01:58: start X-correlation... INFO @ Sun, 21 Jun 2020 17:01:58: end of X-cor INFO @ Sun, 21 Jun 2020 17:01:58: #2 finished! INFO @ Sun, 21 Jun 2020 17:01:58: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 17:01:58: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 17:01:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.05_model.r INFO @ Sun, 21 Jun 2020 17:01:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:01:58: #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 17:02:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.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 17:02:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:02:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:02:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:02:10: 1000000 INFO @ Sun, 21 Jun 2020 17:02:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:02:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:02:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.05_summits.bed INFO @ Sun, 21 Jun 2020 17:02:12: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (4119 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:02:16: 2000000 INFO @ Sun, 21 Jun 2020 17:02:21: 3000000 INFO @ Sun, 21 Jun 2020 17:02:27: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:02:27: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:02:27: #1 total tags in treatment: 3961010 INFO @ Sun, 21 Jun 2020 17:02:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:02:27: #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 17:02:28: #1 tags after filtering in treatment: 3960631 INFO @ Sun, 21 Jun 2020 17:02:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:02:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:02:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:02:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:02:28: #2 number of paired peaks: 1993 INFO @ Sun, 21 Jun 2020 17:02:28: start model_add_line... INFO @ Sun, 21 Jun 2020 17:02:28: start X-correlation... INFO @ Sun, 21 Jun 2020 17:02:28: end of X-cor INFO @ Sun, 21 Jun 2020 17:02:28: #2 finished! INFO @ Sun, 21 Jun 2020 17:02:28: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 17:02:28: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 17:02:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.10_model.r INFO @ Sun, 21 Jun 2020 17:02:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:02:28: #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 17:02:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.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 17:02:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:02:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:02:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:02:40: 1000000 INFO @ Sun, 21 Jun 2020 17:02:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:02:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:02:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.10_summits.bed INFO @ Sun, 21 Jun 2020 17:02:41: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (2047 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:02:46: 2000000 INFO @ Sun, 21 Jun 2020 17:02:51: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:02:57: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:02:57: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:02:57: #1 total tags in treatment: 3961010 INFO @ Sun, 21 Jun 2020 17:02:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:02:57: #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 17:02:58: #1 tags after filtering in treatment: 3960631 INFO @ Sun, 21 Jun 2020 17:02:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:02:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:02:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:02:58: #2 number of paired peaks: 1993 INFO @ Sun, 21 Jun 2020 17:02:58: start model_add_line... INFO @ Sun, 21 Jun 2020 17:02:59: start X-correlation... INFO @ Sun, 21 Jun 2020 17:02:59: end of X-cor INFO @ Sun, 21 Jun 2020 17:02:59: #2 finished! INFO @ Sun, 21 Jun 2020 17:02:59: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 17:02:59: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 17:02:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.20_model.r INFO @ Sun, 21 Jun 2020 17:02:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:02:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:03:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:03:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:03:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:03:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013042/SRX013042.20_summits.bed INFO @ Sun, 21 Jun 2020 17:03:12: Done! pass1 - making usageList (23 chroms): 1 millis pass2 - checking and writing primary data (430 records, 4 fields): 3 millis CompletedMACS2peakCalling