Job ID = 6529781 SRX = SRX4798858 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: 00:03:34 16089303 reads; of these: 16089303 (100.00%) were unpaired; of these: 1951159 (12.13%) aligned 0 times 12759493 (79.30%) aligned exactly 1 time 1378651 (8.57%) aligned >1 times 87.87% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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] 1303679 / 14138144 = 0.0922 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 03:05:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.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 03:05:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:05:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:05:59: 1000000 INFO @ Tue, 30 Jun 2020 03:06:06: 2000000 INFO @ Tue, 30 Jun 2020 03:06:13: 3000000 INFO @ Tue, 30 Jun 2020 03:06:20: 4000000 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 03:06:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.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 03:06:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:06:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:06:27: 5000000 INFO @ Tue, 30 Jun 2020 03:06:30: 1000000 INFO @ Tue, 30 Jun 2020 03:06:34: 6000000 INFO @ Tue, 30 Jun 2020 03:06:37: 2000000 INFO @ Tue, 30 Jun 2020 03:06:42: 7000000 INFO @ Tue, 30 Jun 2020 03:06:45: 3000000 INFO @ Tue, 30 Jun 2020 03:06:49: 8000000 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 03:06:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.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 03:06:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:06:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:06:52: 4000000 INFO @ Tue, 30 Jun 2020 03:06:56: 9000000 INFO @ Tue, 30 Jun 2020 03:07:00: 5000000 INFO @ Tue, 30 Jun 2020 03:07:00: 1000000 INFO @ Tue, 30 Jun 2020 03:07:03: 10000000 INFO @ Tue, 30 Jun 2020 03:07:08: 6000000 INFO @ Tue, 30 Jun 2020 03:07:08: 2000000 INFO @ Tue, 30 Jun 2020 03:07:12: 11000000 INFO @ Tue, 30 Jun 2020 03:07:15: 7000000 INFO @ Tue, 30 Jun 2020 03:07:16: 3000000 INFO @ Tue, 30 Jun 2020 03:07:20: 12000000 INFO @ Tue, 30 Jun 2020 03:07:23: 8000000 INFO @ Tue, 30 Jun 2020 03:07:24: 4000000 INFO @ Tue, 30 Jun 2020 03:07:26: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:07:26: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:07:26: #1 total tags in treatment: 12834465 INFO @ Tue, 30 Jun 2020 03:07:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:07:26: #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 03:07:27: #1 tags after filtering in treatment: 12834427 INFO @ Tue, 30 Jun 2020 03:07:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:07:27: #1 finished! INFO @ Tue, 30 Jun 2020 03:07:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:07:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:07:28: #2 number of paired peaks: 111 WARNING @ Tue, 30 Jun 2020 03:07:28: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Tue, 30 Jun 2020 03:07:28: start model_add_line... INFO @ Tue, 30 Jun 2020 03:07:28: start X-correlation... INFO @ Tue, 30 Jun 2020 03:07:28: end of X-cor INFO @ Tue, 30 Jun 2020 03:07:28: #2 finished! INFO @ Tue, 30 Jun 2020 03:07:28: #2 predicted fragment length is 167 bps INFO @ Tue, 30 Jun 2020 03:07:28: #2 alternative fragment length(s) may be 167,184 bps INFO @ Tue, 30 Jun 2020 03:07:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.05_model.r INFO @ Tue, 30 Jun 2020 03:07:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:07:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:07:30: 9000000 INFO @ Tue, 30 Jun 2020 03:07:31: 5000000 INFO @ Tue, 30 Jun 2020 03:07:37: 10000000 INFO @ Tue, 30 Jun 2020 03:07:39: 6000000 INFO @ Tue, 30 Jun 2020 03:07:46: 11000000 INFO @ Tue, 30 Jun 2020 03:07:46: 7000000 INFO @ Tue, 30 Jun 2020 03:07:53: 12000000 INFO @ Tue, 30 Jun 2020 03:07:54: 8000000 INFO @ Tue, 30 Jun 2020 03:07:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:08:00: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:08:00: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:08:00: #1 total tags in treatment: 12834465 INFO @ Tue, 30 Jun 2020 03:08:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:08:00: #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 03:08:01: #1 tags after filtering in treatment: 12834427 INFO @ Tue, 30 Jun 2020 03:08:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:08:01: #1 finished! INFO @ Tue, 30 Jun 2020 03:08:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:08:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:08:01: 9000000 INFO @ Tue, 30 Jun 2020 03:08:01: #2 number of paired peaks: 111 WARNING @ Tue, 30 Jun 2020 03:08:01: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Tue, 30 Jun 2020 03:08:01: start model_add_line... INFO @ Tue, 30 Jun 2020 03:08:01: start X-correlation... INFO @ Tue, 30 Jun 2020 03:08:02: end of X-cor INFO @ Tue, 30 Jun 2020 03:08:02: #2 finished! INFO @ Tue, 30 Jun 2020 03:08:02: #2 predicted fragment length is 167 bps INFO @ Tue, 30 Jun 2020 03:08:02: #2 alternative fragment length(s) may be 167,184 bps INFO @ Tue, 30 Jun 2020 03:08:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.10_model.r INFO @ Tue, 30 Jun 2020 03:08:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:08:03: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:08:08: 10000000 INFO @ Tue, 30 Jun 2020 03:08:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:08:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:08:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.05_summits.bed INFO @ Tue, 30 Jun 2020 03:08:13: Done! pass1 - making usageList (115 chroms): 2 millis pass2 - checking and writing primary data (6093 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:08:16: 11000000 INFO @ Tue, 30 Jun 2020 03:08:23: 12000000 INFO @ Tue, 30 Jun 2020 03:08:29: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:08:29: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:08:29: #1 total tags in treatment: 12834465 INFO @ Tue, 30 Jun 2020 03:08:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:08:29: #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 03:08:30: #1 tags after filtering in treatment: 12834427 INFO @ Tue, 30 Jun 2020 03:08:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:08:30: #1 finished! INFO @ Tue, 30 Jun 2020 03:08:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:08:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:08:31: #2 number of paired peaks: 111 WARNING @ Tue, 30 Jun 2020 03:08:31: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Tue, 30 Jun 2020 03:08:31: start model_add_line... INFO @ Tue, 30 Jun 2020 03:08:31: start X-correlation... INFO @ Tue, 30 Jun 2020 03:08:31: end of X-cor INFO @ Tue, 30 Jun 2020 03:08:31: #2 finished! INFO @ Tue, 30 Jun 2020 03:08:31: #2 predicted fragment length is 167 bps INFO @ Tue, 30 Jun 2020 03:08:31: #2 alternative fragment length(s) may be 167,184 bps INFO @ Tue, 30 Jun 2020 03:08:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.20_model.r INFO @ Tue, 30 Jun 2020 03:08:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:08:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:08:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:08:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:08:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:08:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.10_summits.bed INFO @ Tue, 30 Jun 2020 03:08:46: Done! pass1 - making usageList (80 chroms): 1 millis pass2 - checking and writing primary data (2008 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:08:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:09:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:09:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:09:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798858/SRX4798858.20_summits.bed INFO @ Tue, 30 Jun 2020 03:09:14: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (232 records, 4 fields): 4 millis CompletedMACS2peakCalling