Job ID = 6529479 SRX = SRX287747 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: 00:03:56 14436912 reads; of these: 14436912 (100.00%) were unpaired; of these: 2185544 (15.14%) aligned 0 times 9303079 (64.44%) aligned exactly 1 time 2948289 (20.42%) aligned >1 times 84.86% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 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] 1182146 / 12251368 = 0.0965 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 02:04:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.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 02:04:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:04:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:04:58: 1000000 INFO @ Tue, 30 Jun 2020 02:05:04: 2000000 INFO @ Tue, 30 Jun 2020 02:05:11: 3000000 INFO @ Tue, 30 Jun 2020 02:05:17: 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 02:05:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.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 02:05:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:05:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:05:23: 5000000 INFO @ Tue, 30 Jun 2020 02:05:28: 1000000 INFO @ Tue, 30 Jun 2020 02:05:30: 6000000 INFO @ Tue, 30 Jun 2020 02:05:35: 2000000 INFO @ Tue, 30 Jun 2020 02:05:36: 7000000 INFO @ Tue, 30 Jun 2020 02:05:42: 3000000 INFO @ Tue, 30 Jun 2020 02:05:43: 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 02:05:49: 4000000 INFO @ Tue, 30 Jun 2020 02:05:50: 9000000 INFO @ Tue, 30 Jun 2020 02:05:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.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 02:05:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:05:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:05:56: 10000000 INFO @ Tue, 30 Jun 2020 02:05:57: 5000000 INFO @ Tue, 30 Jun 2020 02:05:58: 1000000 INFO @ Tue, 30 Jun 2020 02:06:03: 11000000 INFO @ Tue, 30 Jun 2020 02:06:03: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:06:03: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:06:03: #1 total tags in treatment: 11069222 INFO @ Tue, 30 Jun 2020 02:06:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:06:03: #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 02:06:04: 6000000 INFO @ Tue, 30 Jun 2020 02:06:04: #1 tags after filtering in treatment: 11069221 INFO @ Tue, 30 Jun 2020 02:06:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:06:04: #1 finished! INFO @ Tue, 30 Jun 2020 02:06:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:06:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:06:05: #2 number of paired peaks: 596 WARNING @ Tue, 30 Jun 2020 02:06:05: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Tue, 30 Jun 2020 02:06:05: start model_add_line... INFO @ Tue, 30 Jun 2020 02:06:05: start X-correlation... INFO @ Tue, 30 Jun 2020 02:06:05: end of X-cor INFO @ Tue, 30 Jun 2020 02:06:05: #2 finished! INFO @ Tue, 30 Jun 2020 02:06:05: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:06:05: #2 alternative fragment length(s) may be 4,48,581 bps INFO @ Tue, 30 Jun 2020 02:06:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.05_model.r WARNING @ Tue, 30 Jun 2020 02:06:05: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:06:05: #2 You may need to consider one of the other alternative d(s): 4,48,581 WARNING @ Tue, 30 Jun 2020 02:06:05: #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 02:06:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:06:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:06:05: 2000000 INFO @ Tue, 30 Jun 2020 02:06:11: 7000000 INFO @ Tue, 30 Jun 2020 02:06:12: 3000000 INFO @ Tue, 30 Jun 2020 02:06:18: 8000000 INFO @ Tue, 30 Jun 2020 02:06:20: 4000000 INFO @ Tue, 30 Jun 2020 02:06:26: 9000000 INFO @ Tue, 30 Jun 2020 02:06:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:06:27: 5000000 INFO @ Tue, 30 Jun 2020 02:06:33: 10000000 INFO @ Tue, 30 Jun 2020 02:06:34: 6000000 INFO @ Tue, 30 Jun 2020 02:06:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:06:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:06:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.05_summits.bed INFO @ Tue, 30 Jun 2020 02:06:37: Done! pass1 - making usageList (532 chroms): 1 millis pass2 - checking and writing primary data (2001 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:06:40: 11000000 INFO @ Tue, 30 Jun 2020 02:06:41: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:06:41: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:06:41: #1 total tags in treatment: 11069222 INFO @ Tue, 30 Jun 2020 02:06:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:06:41: #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 02:06:41: #1 tags after filtering in treatment: 11069221 INFO @ Tue, 30 Jun 2020 02:06:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:06:41: #1 finished! INFO @ Tue, 30 Jun 2020 02:06:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:06:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:06:41: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:06:42: #2 number of paired peaks: 596 WARNING @ Tue, 30 Jun 2020 02:06:42: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Tue, 30 Jun 2020 02:06:42: start model_add_line... INFO @ Tue, 30 Jun 2020 02:06:42: start X-correlation... INFO @ Tue, 30 Jun 2020 02:06:42: end of X-cor INFO @ Tue, 30 Jun 2020 02:06:42: #2 finished! INFO @ Tue, 30 Jun 2020 02:06:42: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:06:42: #2 alternative fragment length(s) may be 4,48,581 bps INFO @ Tue, 30 Jun 2020 02:06:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.10_model.r WARNING @ Tue, 30 Jun 2020 02:06:42: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:06:42: #2 You may need to consider one of the other alternative d(s): 4,48,581 WARNING @ Tue, 30 Jun 2020 02:06:42: #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 02:06:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:06:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:06:48: 8000000 INFO @ Tue, 30 Jun 2020 02:06:55: 9000000 INFO @ Tue, 30 Jun 2020 02:07:02: 10000000 INFO @ Tue, 30 Jun 2020 02:07:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:07:09: 11000000 INFO @ Tue, 30 Jun 2020 02:07:09: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:07:09: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:07:09: #1 total tags in treatment: 11069222 INFO @ Tue, 30 Jun 2020 02:07:09: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:07:09: #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 02:07:10: #1 tags after filtering in treatment: 11069221 INFO @ Tue, 30 Jun 2020 02:07:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:07:10: #1 finished! INFO @ Tue, 30 Jun 2020 02:07:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:07:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:07:11: #2 number of paired peaks: 596 WARNING @ Tue, 30 Jun 2020 02:07:11: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Tue, 30 Jun 2020 02:07:11: start model_add_line... INFO @ Tue, 30 Jun 2020 02:07:11: start X-correlation... INFO @ Tue, 30 Jun 2020 02:07:11: end of X-cor INFO @ Tue, 30 Jun 2020 02:07:11: #2 finished! INFO @ Tue, 30 Jun 2020 02:07:11: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:07:11: #2 alternative fragment length(s) may be 4,48,581 bps INFO @ Tue, 30 Jun 2020 02:07:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.20_model.r WARNING @ Tue, 30 Jun 2020 02:07:11: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:07:11: #2 You may need to consider one of the other alternative d(s): 4,48,581 WARNING @ Tue, 30 Jun 2020 02:07:11: #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 02:07:11: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:07:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:07:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:07:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:07:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.10_summits.bed INFO @ Tue, 30 Jun 2020 02:07:14: Done! pass1 - making usageList (459 chroms): 2 millis pass2 - checking and writing primary data (1618 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:07:32: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:07:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:07:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:07:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287747/SRX287747.20_summits.bed INFO @ Tue, 30 Jun 2020 02:07:43: Done! pass1 - making usageList (278 chroms): 1 millis pass2 - checking and writing primary data (534 records, 4 fields): 9 millis CompletedMACS2peakCalling