Job ID = 6529176 SRX = SRX027389 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: 00:01:27 7157458 reads; of these: 7157458 (100.00%) were unpaired; of these: 269916 (3.77%) aligned 0 times 5942776 (83.03%) aligned exactly 1 time 944766 (13.20%) aligned >1 times 96.23% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 356135 / 6887542 = 0.0517 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 02:02:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.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 02:02:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:02:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:02:28: 1000000 INFO @ Tue, 30 Jun 2020 02:02:33: 2000000 INFO @ Tue, 30 Jun 2020 02:02:37: 3000000 INFO @ Tue, 30 Jun 2020 02:02:41: 4000000 INFO @ Tue, 30 Jun 2020 02:02:46: 5000000 INFO @ Tue, 30 Jun 2020 02:02:51: 6000000 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 02:02:53: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:02:53: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:02:53: #1 total tags in treatment: 6531407 INFO @ Tue, 30 Jun 2020 02:02:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:02:53: #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 02:02:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.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 02:02:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:02:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:02:54: #1 tags after filtering in treatment: 6531228 INFO @ Tue, 30 Jun 2020 02:02:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:02:54: #1 finished! INFO @ Tue, 30 Jun 2020 02:02:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:02:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:02:54: #2 number of paired peaks: 173 WARNING @ Tue, 30 Jun 2020 02:02:54: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Tue, 30 Jun 2020 02:02:54: start model_add_line... INFO @ Tue, 30 Jun 2020 02:02:54: start X-correlation... INFO @ Tue, 30 Jun 2020 02:02:54: end of X-cor INFO @ Tue, 30 Jun 2020 02:02:54: #2 finished! INFO @ Tue, 30 Jun 2020 02:02:54: #2 predicted fragment length is 99 bps INFO @ Tue, 30 Jun 2020 02:02:54: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 30 Jun 2020 02:02:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.05_model.r INFO @ Tue, 30 Jun 2020 02:02:54: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:02:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:02:58: 1000000 INFO @ Tue, 30 Jun 2020 02:03:02: 2000000 INFO @ Tue, 30 Jun 2020 02:03:07: 3000000 INFO @ Tue, 30 Jun 2020 02:03:07: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:03:11: 4000000 INFO @ Tue, 30 Jun 2020 02:03:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:03:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:03:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.05_summits.bed INFO @ Tue, 30 Jun 2020 02:03:15: Done! pass1 - making usageList (223 chroms): 2 millis pass2 - checking and writing primary data (8938 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:03:16: 5000000 INFO @ Tue, 30 Jun 2020 02:03:21: 6000000 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 02:03:23: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:03:23: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:03:23: #1 total tags in treatment: 6531407 INFO @ Tue, 30 Jun 2020 02:03:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:03:23: #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 02:03:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.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 02:03:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:03:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:03:24: #1 tags after filtering in treatment: 6531228 INFO @ Tue, 30 Jun 2020 02:03:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:03:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:03:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:03:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:03:24: #2 number of paired peaks: 173 WARNING @ Tue, 30 Jun 2020 02:03:24: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Tue, 30 Jun 2020 02:03:24: start model_add_line... INFO @ Tue, 30 Jun 2020 02:03:24: start X-correlation... INFO @ Tue, 30 Jun 2020 02:03:24: end of X-cor INFO @ Tue, 30 Jun 2020 02:03:24: #2 finished! INFO @ Tue, 30 Jun 2020 02:03:24: #2 predicted fragment length is 99 bps INFO @ Tue, 30 Jun 2020 02:03:24: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 30 Jun 2020 02:03:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.10_model.r INFO @ Tue, 30 Jun 2020 02:03:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:03:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:03:28: 1000000 INFO @ Tue, 30 Jun 2020 02:03:33: 2000000 INFO @ Tue, 30 Jun 2020 02:03:37: 3000000 INFO @ Tue, 30 Jun 2020 02:03:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:03:42: 4000000 INFO @ Tue, 30 Jun 2020 02:03:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.10_summits.bed INFO @ Tue, 30 Jun 2020 02:03:45: Done! pass1 - making usageList (95 chroms): 1 millis pass2 - checking and writing primary data (1313 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:03:46: 5000000 INFO @ Tue, 30 Jun 2020 02:03:51: 6000000 INFO @ Tue, 30 Jun 2020 02:03:54: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:03:54: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:03:54: #1 total tags in treatment: 6531407 INFO @ Tue, 30 Jun 2020 02:03:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:03:54: #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 02:03:54: #1 tags after filtering in treatment: 6531228 INFO @ Tue, 30 Jun 2020 02:03:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:03:54: #1 finished! INFO @ Tue, 30 Jun 2020 02:03:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:03:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:03:55: #2 number of paired peaks: 173 WARNING @ Tue, 30 Jun 2020 02:03:55: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Tue, 30 Jun 2020 02:03:55: start model_add_line... INFO @ Tue, 30 Jun 2020 02:03:55: start X-correlation... INFO @ Tue, 30 Jun 2020 02:03:55: end of X-cor INFO @ Tue, 30 Jun 2020 02:03:55: #2 finished! INFO @ Tue, 30 Jun 2020 02:03:55: #2 predicted fragment length is 99 bps INFO @ Tue, 30 Jun 2020 02:03:55: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 30 Jun 2020 02:03:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.20_model.r INFO @ Tue, 30 Jun 2020 02:03:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:03:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:04:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:04:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:04:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:04:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX027389/SRX027389.20_summits.bed INFO @ Tue, 30 Jun 2020 02:04:17: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (80 records, 4 fields): 1 millis CompletedMACS2peakCalling