Job ID = 5720926 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,960,884 reads read : 9,960,884 reads written : 9,960,884 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:03:00 9960884 reads; of these: 9960884 (100.00%) were unpaired; of these: 1649066 (16.56%) aligned 0 times 5050543 (50.70%) aligned exactly 1 time 3261275 (32.74%) aligned >1 times 83.44% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2795626 / 8311818 = 0.3363 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 @ Thu, 16 Apr 2020 03:24:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.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 @ Thu, 16 Apr 2020 03:24:57: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:24:57: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:25:01: 1000000 INFO @ Thu, 16 Apr 2020 03:25:06: 2000000 INFO @ Thu, 16 Apr 2020 03:25:11: 3000000 INFO @ Thu, 16 Apr 2020 03:25:16: 4000000 INFO @ Thu, 16 Apr 2020 03:25:21: 5000000 INFO @ Thu, 16 Apr 2020 03:25:23: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:25:23: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:25:23: #1 total tags in treatment: 5516192 INFO @ Thu, 16 Apr 2020 03:25:23: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:25:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 03:25:23: #1 tags after filtering in treatment: 5516192 INFO @ Thu, 16 Apr 2020 03:25:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:25:23: #1 finished! INFO @ Thu, 16 Apr 2020 03:25:23: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:25:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:25:24: #2 number of paired peaks: 269 WARNING @ Thu, 16 Apr 2020 03:25:24: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Thu, 16 Apr 2020 03:25:24: start model_add_line... INFO @ Thu, 16 Apr 2020 03:25:24: start X-correlation... INFO @ Thu, 16 Apr 2020 03:25:24: end of X-cor INFO @ Thu, 16 Apr 2020 03:25:24: #2 finished! INFO @ Thu, 16 Apr 2020 03:25:24: #2 predicted fragment length is 51 bps INFO @ Thu, 16 Apr 2020 03:25:24: #2 alternative fragment length(s) may be 51 bps INFO @ Thu, 16 Apr 2020 03:25:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.05_model.r WARNING @ Thu, 16 Apr 2020 03:25:24: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:25:24: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Thu, 16 Apr 2020 03:25:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 03:25:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:25:24: #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 @ Thu, 16 Apr 2020 03:25:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.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 @ Thu, 16 Apr 2020 03:25:27: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:25:27: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:25:31: 1000000 INFO @ Thu, 16 Apr 2020 03:25:35: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:25:36: 2000000 INFO @ Thu, 16 Apr 2020 03:25:41: 3000000 INFO @ Thu, 16 Apr 2020 03:25:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:25:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:25:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.05_summits.bed INFO @ Thu, 16 Apr 2020 03:25:41: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1217 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:25:46: 4000000 INFO @ Thu, 16 Apr 2020 03:25:50: 5000000 INFO @ Thu, 16 Apr 2020 03:25:53: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:25:53: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:25:53: #1 total tags in treatment: 5516192 INFO @ Thu, 16 Apr 2020 03:25:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:25:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 03:25:53: #1 tags after filtering in treatment: 5516192 INFO @ Thu, 16 Apr 2020 03:25:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:25:53: #1 finished! INFO @ Thu, 16 Apr 2020 03:25:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:25:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:25:53: #2 number of paired peaks: 269 WARNING @ Thu, 16 Apr 2020 03:25:53: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Thu, 16 Apr 2020 03:25:53: start model_add_line... INFO @ Thu, 16 Apr 2020 03:25:53: start X-correlation... INFO @ Thu, 16 Apr 2020 03:25:53: end of X-cor INFO @ Thu, 16 Apr 2020 03:25:53: #2 finished! INFO @ Thu, 16 Apr 2020 03:25:53: #2 predicted fragment length is 51 bps INFO @ Thu, 16 Apr 2020 03:25:53: #2 alternative fragment length(s) may be 51 bps INFO @ Thu, 16 Apr 2020 03:25:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.10_model.r WARNING @ Thu, 16 Apr 2020 03:25:53: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:25:53: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Thu, 16 Apr 2020 03:25:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 03:25:53: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:25:53: #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 @ Thu, 16 Apr 2020 03:25:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.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 @ Thu, 16 Apr 2020 03:25:57: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:25:57: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:26:02: 1000000 INFO @ Thu, 16 Apr 2020 03:26:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:26:07: 2000000 INFO @ Thu, 16 Apr 2020 03:26:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:26:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:26:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.10_summits.bed INFO @ Thu, 16 Apr 2020 03:26:11: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (842 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:26:11: 3000000 INFO @ Thu, 16 Apr 2020 03:26:16: 4000000 INFO @ Thu, 16 Apr 2020 03:26:21: 5000000 INFO @ Thu, 16 Apr 2020 03:26:24: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:26:24: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:26:24: #1 total tags in treatment: 5516192 INFO @ Thu, 16 Apr 2020 03:26:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:26:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 03:26:24: #1 tags after filtering in treatment: 5516192 INFO @ Thu, 16 Apr 2020 03:26:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:26:24: #1 finished! INFO @ Thu, 16 Apr 2020 03:26:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:26:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:26:24: #2 number of paired peaks: 269 WARNING @ Thu, 16 Apr 2020 03:26:24: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Thu, 16 Apr 2020 03:26:24: start model_add_line... INFO @ Thu, 16 Apr 2020 03:26:24: start X-correlation... INFO @ Thu, 16 Apr 2020 03:26:24: end of X-cor INFO @ Thu, 16 Apr 2020 03:26:24: #2 finished! INFO @ Thu, 16 Apr 2020 03:26:24: #2 predicted fragment length is 51 bps INFO @ Thu, 16 Apr 2020 03:26:24: #2 alternative fragment length(s) may be 51 bps INFO @ Thu, 16 Apr 2020 03:26:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.20_model.r WARNING @ Thu, 16 Apr 2020 03:26:24: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:26:24: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Thu, 16 Apr 2020 03:26:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 03:26:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:26:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:26:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:26:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:26:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:26:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386727/SRX6386727.20_summits.bed INFO @ Thu, 16 Apr 2020 03:26:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (400 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。