Job ID = 6529804 SRX = SRX4933887 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: 00:03:10 10269012 reads; of these: 10269012 (100.00%) were unpaired; of these: 459035 (4.47%) aligned 0 times 6732986 (65.57%) aligned exactly 1 time 3076991 (29.96%) aligned >1 times 95.53% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 1339741 / 9809977 = 0.1366 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 02:51:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.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 02:51:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:51:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:51:07: 1000000 INFO @ Tue, 30 Jun 2020 02:51:13: 2000000 INFO @ Tue, 30 Jun 2020 02:51:20: 3000000 INFO @ Tue, 30 Jun 2020 02:51:27: 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 02:51:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.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 02:51:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:51:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:51:35: 5000000 INFO @ Tue, 30 Jun 2020 02:51:38: 1000000 INFO @ Tue, 30 Jun 2020 02:51:42: 6000000 INFO @ Tue, 30 Jun 2020 02:51:45: 2000000 INFO @ Tue, 30 Jun 2020 02:51:50: 7000000 INFO @ Tue, 30 Jun 2020 02:51:53: 3000000 INFO @ Tue, 30 Jun 2020 02:51:57: 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 02:52:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.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 02:52:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:00: 4000000 INFO @ Tue, 30 Jun 2020 02:52:01: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:52:01: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:52:01: #1 total tags in treatment: 8470236 INFO @ Tue, 30 Jun 2020 02:52:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:52:01: #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 02:52:02: #1 tags after filtering in treatment: 8470231 INFO @ Tue, 30 Jun 2020 02:52:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:52:02: #1 finished! INFO @ Tue, 30 Jun 2020 02:52:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:52:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:52:02: #2 number of paired peaks: 489 WARNING @ Tue, 30 Jun 2020 02:52:02: Fewer paired peaks (489) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 489 pairs to build model! INFO @ Tue, 30 Jun 2020 02:52:02: start model_add_line... INFO @ Tue, 30 Jun 2020 02:52:02: start X-correlation... INFO @ Tue, 30 Jun 2020 02:52:02: end of X-cor INFO @ Tue, 30 Jun 2020 02:52:02: #2 finished! INFO @ Tue, 30 Jun 2020 02:52:02: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 02:52:02: #2 alternative fragment length(s) may be 2,51 bps INFO @ Tue, 30 Jun 2020 02:52:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.05_model.r WARNING @ Tue, 30 Jun 2020 02:52:02: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:52:02: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Tue, 30 Jun 2020 02:52:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:52:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:52:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:52:08: 5000000 INFO @ Tue, 30 Jun 2020 02:52:08: 1000000 INFO @ Tue, 30 Jun 2020 02:52:15: 6000000 INFO @ Tue, 30 Jun 2020 02:52:16: 2000000 INFO @ Tue, 30 Jun 2020 02:52:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:52:23: 7000000 INFO @ Tue, 30 Jun 2020 02:52:24: 3000000 INFO @ Tue, 30 Jun 2020 02:52:30: 8000000 INFO @ Tue, 30 Jun 2020 02:52:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:52:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:52:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.05_summits.bed INFO @ Tue, 30 Jun 2020 02:52:32: Done! pass1 - making usageList (594 chroms): 2 millis pass2 - checking and writing primary data (2182 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:52:32: 4000000 INFO @ Tue, 30 Jun 2020 02:52:34: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:52:34: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:52:34: #1 total tags in treatment: 8470236 INFO @ Tue, 30 Jun 2020 02:52:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:52:34: #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 02:52:34: #1 tags after filtering in treatment: 8470231 INFO @ Tue, 30 Jun 2020 02:52:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:52:34: #1 finished! INFO @ Tue, 30 Jun 2020 02:52:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:52:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:52:35: #2 number of paired peaks: 489 WARNING @ Tue, 30 Jun 2020 02:52:35: Fewer paired peaks (489) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 489 pairs to build model! INFO @ Tue, 30 Jun 2020 02:52:35: start model_add_line... INFO @ Tue, 30 Jun 2020 02:52:35: start X-correlation... INFO @ Tue, 30 Jun 2020 02:52:35: end of X-cor INFO @ Tue, 30 Jun 2020 02:52:35: #2 finished! INFO @ Tue, 30 Jun 2020 02:52:35: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 02:52:35: #2 alternative fragment length(s) may be 2,51 bps INFO @ Tue, 30 Jun 2020 02:52:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.10_model.r WARNING @ Tue, 30 Jun 2020 02:52:35: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:52:35: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Tue, 30 Jun 2020 02:52:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:52:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:52:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:52:40: 5000000 INFO @ Tue, 30 Jun 2020 02:52:48: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:52:55: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:52:56: 7000000 INFO @ Tue, 30 Jun 2020 02:53:04: 8000000 INFO @ Tue, 30 Jun 2020 02:53:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:53:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:53:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.10_summits.bed INFO @ Tue, 30 Jun 2020 02:53:05: Done! pass1 - making usageList (430 chroms): 1 millis pass2 - checking and writing primary data (1163 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:53:08: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:53:08: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:53:08: #1 total tags in treatment: 8470236 INFO @ Tue, 30 Jun 2020 02:53:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:53:08: #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 02:53:08: #1 tags after filtering in treatment: 8470231 INFO @ Tue, 30 Jun 2020 02:53:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:53:08: #1 finished! INFO @ Tue, 30 Jun 2020 02:53:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:53:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:53:09: #2 number of paired peaks: 489 WARNING @ Tue, 30 Jun 2020 02:53:09: Fewer paired peaks (489) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 489 pairs to build model! INFO @ Tue, 30 Jun 2020 02:53:09: start model_add_line... INFO @ Tue, 30 Jun 2020 02:53:09: start X-correlation... INFO @ Tue, 30 Jun 2020 02:53:09: end of X-cor INFO @ Tue, 30 Jun 2020 02:53:09: #2 finished! INFO @ Tue, 30 Jun 2020 02:53:09: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 02:53:09: #2 alternative fragment length(s) may be 2,51 bps INFO @ Tue, 30 Jun 2020 02:53:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.20_model.r WARNING @ Tue, 30 Jun 2020 02:53:09: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:53:09: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Tue, 30 Jun 2020 02:53:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:53:09: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:53:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:53:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:53:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:53:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:53:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933887/SRX4933887.20_summits.bed INFO @ Tue, 30 Jun 2020 02:53:38: Done! pass1 - making usageList (160 chroms): 1 millis pass2 - checking and writing primary data (285 records, 4 fields): 6 millis CompletedMACS2peakCalling