Job ID = 6529516 SRX = SRX287886 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: 00:06:21 21494133 reads; of these: 21494133 (100.00%) were unpaired; of these: 1544555 (7.19%) aligned 0 times 13572895 (63.15%) aligned exactly 1 time 6376683 (29.67%) aligned >1 times 92.81% overall alignment rate Time searching: 00:06:21 Overall time: 00:06:21 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 12 files... [bam_rmdupse_core] 3736815 / 19949578 = 0.1873 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 02:57:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.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 02:57:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:57:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:57:05: 1000000 INFO @ Tue, 30 Jun 2020 02:57:10: 2000000 INFO @ Tue, 30 Jun 2020 02:57:15: 3000000 INFO @ Tue, 30 Jun 2020 02:57:20: 4000000 INFO @ Tue, 30 Jun 2020 02:57:25: 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 02:57:29: 6000000 INFO @ Tue, 30 Jun 2020 02:57:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.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 02:57:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:57:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:57:34: 7000000 INFO @ Tue, 30 Jun 2020 02:57:35: 1000000 INFO @ Tue, 30 Jun 2020 02:57:39: 8000000 INFO @ Tue, 30 Jun 2020 02:57:40: 2000000 INFO @ Tue, 30 Jun 2020 02:57:44: 9000000 INFO @ Tue, 30 Jun 2020 02:57:45: 3000000 INFO @ Tue, 30 Jun 2020 02:57:49: 10000000 INFO @ Tue, 30 Jun 2020 02:57:50: 4000000 INFO @ Tue, 30 Jun 2020 02:57:54: 11000000 INFO @ Tue, 30 Jun 2020 02:57:55: 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 02:57:58: 12000000 INFO @ Tue, 30 Jun 2020 02:58:00: 6000000 INFO @ Tue, 30 Jun 2020 02:58:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.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 02:58:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:04: 13000000 INFO @ Tue, 30 Jun 2020 02:58:04: 7000000 INFO @ Tue, 30 Jun 2020 02:58:05: 1000000 INFO @ Tue, 30 Jun 2020 02:58:09: 14000000 INFO @ Tue, 30 Jun 2020 02:58:09: 8000000 INFO @ Tue, 30 Jun 2020 02:58:10: 2000000 INFO @ Tue, 30 Jun 2020 02:58:14: 15000000 INFO @ Tue, 30 Jun 2020 02:58:14: 9000000 INFO @ Tue, 30 Jun 2020 02:58:15: 3000000 INFO @ Tue, 30 Jun 2020 02:58:19: 16000000 INFO @ Tue, 30 Jun 2020 02:58:19: 10000000 INFO @ Tue, 30 Jun 2020 02:58:20: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:58:20: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:58:20: #1 total tags in treatment: 16212763 INFO @ Tue, 30 Jun 2020 02:58:20: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:58:20: #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 02:58:20: 4000000 INFO @ Tue, 30 Jun 2020 02:58:20: #1 tags after filtering in treatment: 16212763 INFO @ Tue, 30 Jun 2020 02:58:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:58:20: #1 finished! INFO @ Tue, 30 Jun 2020 02:58:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:58:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:58:22: #2 number of paired peaks: 753 WARNING @ Tue, 30 Jun 2020 02:58:22: Fewer paired peaks (753) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 753 pairs to build model! INFO @ Tue, 30 Jun 2020 02:58:22: start model_add_line... INFO @ Tue, 30 Jun 2020 02:58:22: start X-correlation... INFO @ Tue, 30 Jun 2020 02:58:22: end of X-cor INFO @ Tue, 30 Jun 2020 02:58:22: #2 finished! INFO @ Tue, 30 Jun 2020 02:58:22: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:58:22: #2 alternative fragment length(s) may be 2,16,35,592 bps INFO @ Tue, 30 Jun 2020 02:58:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.05_model.r WARNING @ Tue, 30 Jun 2020 02:58:22: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:58:22: #2 You may need to consider one of the other alternative d(s): 2,16,35,592 WARNING @ Tue, 30 Jun 2020 02:58:22: #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 02:58:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:58:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:58:24: 11000000 INFO @ Tue, 30 Jun 2020 02:58:25: 5000000 INFO @ Tue, 30 Jun 2020 02:58:29: 12000000 INFO @ Tue, 30 Jun 2020 02:58:30: 6000000 INFO @ Tue, 30 Jun 2020 02:58:34: 13000000 INFO @ Tue, 30 Jun 2020 02:58:35: 7000000 INFO @ Tue, 30 Jun 2020 02:58:39: 14000000 INFO @ Tue, 30 Jun 2020 02:58:40: 8000000 INFO @ Tue, 30 Jun 2020 02:58:44: 15000000 INFO @ Tue, 30 Jun 2020 02:58:45: 9000000 INFO @ Tue, 30 Jun 2020 02:58:49: 16000000 INFO @ Tue, 30 Jun 2020 02:58:49: 10000000 INFO @ Tue, 30 Jun 2020 02:58:50: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:58:50: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:58:50: #1 total tags in treatment: 16212763 INFO @ Tue, 30 Jun 2020 02:58:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:58:50: #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 02:58:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:58:51: #1 tags after filtering in treatment: 16212763 INFO @ Tue, 30 Jun 2020 02:58:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:58:51: #1 finished! INFO @ Tue, 30 Jun 2020 02:58:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:58:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:58:52: #2 number of paired peaks: 753 WARNING @ Tue, 30 Jun 2020 02:58:52: Fewer paired peaks (753) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 753 pairs to build model! INFO @ Tue, 30 Jun 2020 02:58:52: start model_add_line... INFO @ Tue, 30 Jun 2020 02:58:52: start X-correlation... INFO @ Tue, 30 Jun 2020 02:58:52: end of X-cor INFO @ Tue, 30 Jun 2020 02:58:52: #2 finished! INFO @ Tue, 30 Jun 2020 02:58:52: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:58:52: #2 alternative fragment length(s) may be 2,16,35,592 bps INFO @ Tue, 30 Jun 2020 02:58:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.10_model.r WARNING @ Tue, 30 Jun 2020 02:58:52: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:58:52: #2 You may need to consider one of the other alternative d(s): 2,16,35,592 WARNING @ Tue, 30 Jun 2020 02:58:52: #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 02:58:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:58:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:58:54: 11000000 INFO @ Tue, 30 Jun 2020 02:58:59: 12000000 INFO @ Tue, 30 Jun 2020 02:59:05: 13000000 INFO @ Tue, 30 Jun 2020 02:59:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:59:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:59:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.05_summits.bed INFO @ Tue, 30 Jun 2020 02:59:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:59:10: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:59:15: 15000000 INFO @ Tue, 30 Jun 2020 02:59:20: 16000000 INFO @ Tue, 30 Jun 2020 02:59:20: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:59:21: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:59:21: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:59:21: #1 total tags in treatment: 16212763 INFO @ Tue, 30 Jun 2020 02:59:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:59:21: #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 02:59:21: #1 tags after filtering in treatment: 16212763 INFO @ Tue, 30 Jun 2020 02:59:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:59:21: #1 finished! INFO @ Tue, 30 Jun 2020 02:59:21: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:59:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:59:22: #2 number of paired peaks: 753 WARNING @ Tue, 30 Jun 2020 02:59:22: Fewer paired peaks (753) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 753 pairs to build model! INFO @ Tue, 30 Jun 2020 02:59:22: start model_add_line... INFO @ Tue, 30 Jun 2020 02:59:23: start X-correlation... INFO @ Tue, 30 Jun 2020 02:59:23: end of X-cor INFO @ Tue, 30 Jun 2020 02:59:23: #2 finished! INFO @ Tue, 30 Jun 2020 02:59:23: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:59:23: #2 alternative fragment length(s) may be 2,16,35,592 bps INFO @ Tue, 30 Jun 2020 02:59:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.20_model.r WARNING @ Tue, 30 Jun 2020 02:59:23: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:59:23: #2 You may need to consider one of the other alternative d(s): 2,16,35,592 WARNING @ Tue, 30 Jun 2020 02:59:23: #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 02:59:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:59:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:59:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:59:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:59:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.10_summits.bed INFO @ Tue, 30 Jun 2020 02:59:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:59:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:00:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:00:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:00:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287886/SRX287886.20_summits.bed INFO @ Tue, 30 Jun 2020 03:00:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling