Job ID = 6529846 SRX = SRX5243664 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:01:57 8266580 reads; of these: 8266580 (100.00%) were unpaired; of these: 439584 (5.32%) aligned 0 times 6242455 (75.51%) aligned exactly 1 time 1584541 (19.17%) aligned >1 times 94.68% overall alignment rate Time searching: 00:01:57 Overall time: 00:01:57 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] 1358306 / 7826996 = 0.1735 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 @ Tue, 30 Jun 2020 03:04:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.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 @ Tue, 30 Jun 2020 03:04:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:04:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:04:36: 1000000 INFO @ Tue, 30 Jun 2020 03:04:41: 2000000 INFO @ Tue, 30 Jun 2020 03:04:46: 3000000 INFO @ Tue, 30 Jun 2020 03:04:52: 4000000 INFO @ Tue, 30 Jun 2020 03:04:57: 5000000 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 @ Tue, 30 Jun 2020 03:05:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.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 @ Tue, 30 Jun 2020 03:05:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:05:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:05:03: 6000000 INFO @ Tue, 30 Jun 2020 03:05:06: 1000000 INFO @ Tue, 30 Jun 2020 03:05:06: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:05:06: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:05:06: #1 total tags in treatment: 6468690 INFO @ Tue, 30 Jun 2020 03:05:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:05:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:05:07: #1 tags after filtering in treatment: 6468552 INFO @ Tue, 30 Jun 2020 03:05:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:05:07: #1 finished! INFO @ Tue, 30 Jun 2020 03:05:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:05:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:05:07: #2 number of paired peaks: 286 WARNING @ Tue, 30 Jun 2020 03:05:07: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 30 Jun 2020 03:05:07: start model_add_line... INFO @ Tue, 30 Jun 2020 03:05:07: start X-correlation... INFO @ Tue, 30 Jun 2020 03:05:07: end of X-cor INFO @ Tue, 30 Jun 2020 03:05:07: #2 finished! INFO @ Tue, 30 Jun 2020 03:05:07: #2 predicted fragment length is 187 bps INFO @ Tue, 30 Jun 2020 03:05:07: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 30 Jun 2020 03:05:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.05_model.r INFO @ Tue, 30 Jun 2020 03:05:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:05:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:05:11: 2000000 INFO @ Tue, 30 Jun 2020 03:05:17: 3000000 INFO @ Tue, 30 Jun 2020 03:05:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:05:22: 4000000 INFO @ Tue, 30 Jun 2020 03:05:28: 5000000 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 @ Tue, 30 Jun 2020 03:05:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:05:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:05:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.05_summits.bed INFO @ Tue, 30 Jun 2020 03:05:29: Done! pass1 - making usageList (337 chroms): 1 millis pass2 - checking and writing primary data (1382 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:05:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.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 @ Tue, 30 Jun 2020 03:05:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:05:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:05:34: 6000000 INFO @ Tue, 30 Jun 2020 03:05:36: 1000000 INFO @ Tue, 30 Jun 2020 03:05:37: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:05:37: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:05:37: #1 total tags in treatment: 6468690 INFO @ Tue, 30 Jun 2020 03:05:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:05:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:05:37: #1 tags after filtering in treatment: 6468552 INFO @ Tue, 30 Jun 2020 03:05:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:05:37: #1 finished! INFO @ Tue, 30 Jun 2020 03:05:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:05:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:05:37: #2 number of paired peaks: 286 WARNING @ Tue, 30 Jun 2020 03:05:37: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 30 Jun 2020 03:05:37: start model_add_line... INFO @ Tue, 30 Jun 2020 03:05:37: start X-correlation... INFO @ Tue, 30 Jun 2020 03:05:37: end of X-cor INFO @ Tue, 30 Jun 2020 03:05:37: #2 finished! INFO @ Tue, 30 Jun 2020 03:05:37: #2 predicted fragment length is 187 bps INFO @ Tue, 30 Jun 2020 03:05:37: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 30 Jun 2020 03:05:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.10_model.r INFO @ Tue, 30 Jun 2020 03:05:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:05:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:05:41: 2000000 INFO @ Tue, 30 Jun 2020 03:05:47: 3000000 INFO @ Tue, 30 Jun 2020 03:05:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:05:52: 4000000 INFO @ Tue, 30 Jun 2020 03:05:58: 5000000 INFO @ Tue, 30 Jun 2020 03:05:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:05:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:05:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.10_summits.bed INFO @ Tue, 30 Jun 2020 03:05:58: Done! pass1 - making usageList (241 chroms): 1 millis pass2 - checking and writing primary data (478 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:06:03: 6000000 INFO @ Tue, 30 Jun 2020 03:06:06: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:06:06: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:06:06: #1 total tags in treatment: 6468690 INFO @ Tue, 30 Jun 2020 03:06:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:06:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:06:06: #1 tags after filtering in treatment: 6468552 INFO @ Tue, 30 Jun 2020 03:06:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:06:06: #1 finished! INFO @ Tue, 30 Jun 2020 03:06:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:06:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:06:07: #2 number of paired peaks: 286 WARNING @ Tue, 30 Jun 2020 03:06:07: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 30 Jun 2020 03:06:07: start model_add_line... INFO @ Tue, 30 Jun 2020 03:06:07: start X-correlation... INFO @ Tue, 30 Jun 2020 03:06:07: end of X-cor INFO @ Tue, 30 Jun 2020 03:06:07: #2 finished! INFO @ Tue, 30 Jun 2020 03:06:07: #2 predicted fragment length is 187 bps INFO @ Tue, 30 Jun 2020 03:06:07: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 30 Jun 2020 03:06:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.20_model.r INFO @ Tue, 30 Jun 2020 03:06:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:06:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:06:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:06:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:06:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:06:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5243664/SRX5243664.20_summits.bed INFO @ Tue, 30 Jun 2020 03:06:28: Done! pass1 - making usageList (112 chroms): 1 millis pass2 - checking and writing primary data (150 records, 4 fields): 4 millis CompletedMACS2peakCalling