Job ID = 6529207 SRX = SRX041398 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: 00:12:57 47044525 reads; of these: 47044525 (100.00%) were unpaired; of these: 2249924 (4.78%) aligned 0 times 36110872 (76.76%) aligned exactly 1 time 8683729 (18.46%) aligned >1 times 95.22% overall alignment rate Time searching: 00:12:57 Overall time: 00:12:57 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] 30170947 / 44794601 = 0.6735 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 02:17:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.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 02:17:45: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:45: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:51: 1000000 INFO @ Tue, 30 Jun 2020 02:17:56: 2000000 INFO @ Tue, 30 Jun 2020 02:18:01: 3000000 INFO @ Tue, 30 Jun 2020 02:18:06: 4000000 INFO @ Tue, 30 Jun 2020 02:18:11: 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 02:18:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.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 02:18:15: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:18:15: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:18:16: 6000000 INFO @ Tue, 30 Jun 2020 02:18:21: 1000000 INFO @ Tue, 30 Jun 2020 02:18:21: 7000000 INFO @ Tue, 30 Jun 2020 02:18:26: 2000000 INFO @ Tue, 30 Jun 2020 02:18:27: 8000000 INFO @ Tue, 30 Jun 2020 02:18:31: 3000000 INFO @ Tue, 30 Jun 2020 02:18:32: 9000000 INFO @ Tue, 30 Jun 2020 02:18:36: 4000000 INFO @ Tue, 30 Jun 2020 02:18:37: 10000000 INFO @ Tue, 30 Jun 2020 02:18:42: 5000000 INFO @ Tue, 30 Jun 2020 02:18:42: 11000000 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 02:18:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.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 02:18:45: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:18:45: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:18:47: 6000000 INFO @ Tue, 30 Jun 2020 02:18:48: 12000000 INFO @ Tue, 30 Jun 2020 02:18:51: 1000000 INFO @ Tue, 30 Jun 2020 02:18:52: 7000000 INFO @ Tue, 30 Jun 2020 02:18:54: 13000000 INFO @ Tue, 30 Jun 2020 02:18:57: 2000000 INFO @ Tue, 30 Jun 2020 02:18:57: 8000000 INFO @ Tue, 30 Jun 2020 02:18:59: 14000000 INFO @ Tue, 30 Jun 2020 02:19:02: 3000000 INFO @ Tue, 30 Jun 2020 02:19:03: 9000000 INFO @ Tue, 30 Jun 2020 02:19:03: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:19:03: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:19:03: #1 total tags in treatment: 14623654 INFO @ Tue, 30 Jun 2020 02:19:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:19:03: #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 02:19:04: #1 tags after filtering in treatment: 14623647 INFO @ Tue, 30 Jun 2020 02:19:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:19:04: #1 finished! INFO @ Tue, 30 Jun 2020 02:19:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:19:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:19:05: #2 number of paired peaks: 755 WARNING @ Tue, 30 Jun 2020 02:19:05: Fewer paired peaks (755) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 755 pairs to build model! INFO @ Tue, 30 Jun 2020 02:19:05: start model_add_line... INFO @ Tue, 30 Jun 2020 02:19:05: start X-correlation... INFO @ Tue, 30 Jun 2020 02:19:05: end of X-cor INFO @ Tue, 30 Jun 2020 02:19:05: #2 finished! INFO @ Tue, 30 Jun 2020 02:19:05: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:19:05: #2 alternative fragment length(s) may be 2,18,28 bps INFO @ Tue, 30 Jun 2020 02:19:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.05_model.r WARNING @ Tue, 30 Jun 2020 02:19:05: #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 02:19:05: #2 You may need to consider one of the other alternative d(s): 2,18,28 WARNING @ Tue, 30 Jun 2020 02:19:05: #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 02:19:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:19:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:19:08: 10000000 INFO @ Tue, 30 Jun 2020 02:19:08: 4000000 INFO @ Tue, 30 Jun 2020 02:19:13: 11000000 INFO @ Tue, 30 Jun 2020 02:19:13: 5000000 INFO @ Tue, 30 Jun 2020 02:19:18: 6000000 INFO @ Tue, 30 Jun 2020 02:19:19: 12000000 INFO @ Tue, 30 Jun 2020 02:19:24: 7000000 INFO @ Tue, 30 Jun 2020 02:19:24: 13000000 INFO @ Tue, 30 Jun 2020 02:19:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:19:29: 14000000 INFO @ Tue, 30 Jun 2020 02:19:29: 8000000 INFO @ Tue, 30 Jun 2020 02:19:33: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:19:33: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:19:33: #1 total tags in treatment: 14623654 INFO @ Tue, 30 Jun 2020 02:19:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:19:33: #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 02:19:33: #1 tags after filtering in treatment: 14623647 INFO @ Tue, 30 Jun 2020 02:19:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:19:33: #1 finished! INFO @ Tue, 30 Jun 2020 02:19:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:19:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:19:34: 9000000 INFO @ Tue, 30 Jun 2020 02:19:35: #2 number of paired peaks: 755 WARNING @ Tue, 30 Jun 2020 02:19:35: Fewer paired peaks (755) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 755 pairs to build model! INFO @ Tue, 30 Jun 2020 02:19:35: start model_add_line... INFO @ Tue, 30 Jun 2020 02:19:35: start X-correlation... INFO @ Tue, 30 Jun 2020 02:19:35: end of X-cor INFO @ Tue, 30 Jun 2020 02:19:35: #2 finished! INFO @ Tue, 30 Jun 2020 02:19:35: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:19:35: #2 alternative fragment length(s) may be 2,18,28 bps INFO @ Tue, 30 Jun 2020 02:19:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.10_model.r WARNING @ Tue, 30 Jun 2020 02:19:35: #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 02:19:35: #2 You may need to consider one of the other alternative d(s): 2,18,28 WARNING @ Tue, 30 Jun 2020 02:19:35: #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 02:19:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:19:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:19:39: 10000000 INFO @ Tue, 30 Jun 2020 02:19:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:19:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:19:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.05_summits.bed INFO @ Tue, 30 Jun 2020 02:19:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:19:45: 11000000 INFO @ Tue, 30 Jun 2020 02:19:50: 12000000 INFO @ Tue, 30 Jun 2020 02:19:56: 13000000 INFO @ Tue, 30 Jun 2020 02:19:58: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:20:01: 14000000 INFO @ Tue, 30 Jun 2020 02:20:04: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 02:20:04: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 02:20:04: #1 total tags in treatment: 14623654 INFO @ Tue, 30 Jun 2020 02:20:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:04: #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 02:20:05: #1 tags after filtering in treatment: 14623647 INFO @ Tue, 30 Jun 2020 02:20:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:05: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:20:06: #2 number of paired peaks: 755 WARNING @ Tue, 30 Jun 2020 02:20:06: Fewer paired peaks (755) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 755 pairs to build model! INFO @ Tue, 30 Jun 2020 02:20:06: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:06: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:06: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:06: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:06: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:20:06: #2 alternative fragment length(s) may be 2,18,28 bps INFO @ Tue, 30 Jun 2020 02:20:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.20_model.r WARNING @ Tue, 30 Jun 2020 02:20:06: #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 02:20:06: #2 You may need to consider one of the other alternative d(s): 2,18,28 WARNING @ Tue, 30 Jun 2020 02:20:06: #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 02:20:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:20:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:20:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.10_summits.bed INFO @ Tue, 30 Jun 2020 02:20:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:20:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:20:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:20:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:20:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041398/SRX041398.20_summits.bed INFO @ Tue, 30 Jun 2020 02:20:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling