Job ID = 6529417 SRX = SRX2592424 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: 00:09:14 24424359 reads; of these: 24424359 (100.00%) were unpaired; of these: 1854233 (7.59%) aligned 0 times 16810285 (68.83%) aligned exactly 1 time 5759841 (23.58%) aligned >1 times 92.41% overall alignment rate Time searching: 00:09:14 Overall time: 00:09:14 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] 5607530 / 22570126 = 0.2484 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 02:19:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.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 02:19:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:19:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:19:23: 1000000 INFO @ Tue, 30 Jun 2020 02:19:28: 2000000 INFO @ Tue, 30 Jun 2020 02:19:33: 3000000 INFO @ Tue, 30 Jun 2020 02:19:39: 4000000 INFO @ Tue, 30 Jun 2020 02:19:44: 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 02:19:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.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 02:19:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:19:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:19:50: 6000000 INFO @ Tue, 30 Jun 2020 02:19:53: 1000000 INFO @ Tue, 30 Jun 2020 02:19:55: 7000000 INFO @ Tue, 30 Jun 2020 02:19:58: 2000000 INFO @ Tue, 30 Jun 2020 02:20:01: 8000000 INFO @ Tue, 30 Jun 2020 02:20:03: 3000000 INFO @ Tue, 30 Jun 2020 02:20:06: 9000000 INFO @ Tue, 30 Jun 2020 02:20:09: 4000000 INFO @ Tue, 30 Jun 2020 02:20:12: 10000000 INFO @ Tue, 30 Jun 2020 02:20:14: 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 02:20:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.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 02:20:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:20:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:20:17: 11000000 INFO @ Tue, 30 Jun 2020 02:20:19: 6000000 INFO @ Tue, 30 Jun 2020 02:20:22: 12000000 INFO @ Tue, 30 Jun 2020 02:20:22: 1000000 INFO @ Tue, 30 Jun 2020 02:20:25: 7000000 INFO @ Tue, 30 Jun 2020 02:20:28: 13000000 INFO @ Tue, 30 Jun 2020 02:20:28: 2000000 INFO @ Tue, 30 Jun 2020 02:20:30: 8000000 INFO @ Tue, 30 Jun 2020 02:20:34: 3000000 INFO @ Tue, 30 Jun 2020 02:20:34: 14000000 INFO @ Tue, 30 Jun 2020 02:20:36: 9000000 INFO @ Tue, 30 Jun 2020 02:20:39: 15000000 INFO @ Tue, 30 Jun 2020 02:20:39: 4000000 INFO @ Tue, 30 Jun 2020 02:20:42: 10000000 INFO @ Tue, 30 Jun 2020 02:20:44: 16000000 INFO @ Tue, 30 Jun 2020 02:20:45: 5000000 INFO @ Tue, 30 Jun 2020 02:20:47: 11000000 INFO @ Tue, 30 Jun 2020 02:20:50: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:20:50: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:20:50: #1 total tags in treatment: 16962596 INFO @ Tue, 30 Jun 2020 02:20:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:50: #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 02:20:50: #1 tags after filtering in treatment: 16962505 INFO @ Tue, 30 Jun 2020 02:20:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:20:50: 6000000 INFO @ Tue, 30 Jun 2020 02:20:52: #2 number of paired peaks: 217 WARNING @ Tue, 30 Jun 2020 02:20:52: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Tue, 30 Jun 2020 02:20:52: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:52: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:52: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:52: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:52: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:20:52: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 30 Jun 2020 02:20:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.05_model.r WARNING @ Tue, 30 Jun 2020 02:20:52: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:20:52: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 30 Jun 2020 02:20:52: #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 02:20:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:53: 12000000 INFO @ Tue, 30 Jun 2020 02:20:56: 7000000 INFO @ Tue, 30 Jun 2020 02:20:58: 13000000 INFO @ Tue, 30 Jun 2020 02:21:01: 8000000 INFO @ Tue, 30 Jun 2020 02:21:04: 14000000 INFO @ Tue, 30 Jun 2020 02:21:07: 9000000 INFO @ Tue, 30 Jun 2020 02:21:09: 15000000 INFO @ Tue, 30 Jun 2020 02:21:13: 10000000 INFO @ Tue, 30 Jun 2020 02:21:15: 16000000 INFO @ Tue, 30 Jun 2020 02:21:18: 11000000 INFO @ Tue, 30 Jun 2020 02:21:21: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:21:21: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:21:21: #1 total tags in treatment: 16962596 INFO @ Tue, 30 Jun 2020 02:21:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:21:21: #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 02:21:21: #1 tags after filtering in treatment: 16962505 INFO @ Tue, 30 Jun 2020 02:21:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:21:21: #1 finished! INFO @ Tue, 30 Jun 2020 02:21:21: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:21:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:21:23: #2 number of paired peaks: 217 WARNING @ Tue, 30 Jun 2020 02:21:23: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Tue, 30 Jun 2020 02:21:23: start model_add_line... INFO @ Tue, 30 Jun 2020 02:21:23: start X-correlation... INFO @ Tue, 30 Jun 2020 02:21:23: end of X-cor INFO @ Tue, 30 Jun 2020 02:21:23: #2 finished! INFO @ Tue, 30 Jun 2020 02:21:23: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:21:23: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 30 Jun 2020 02:21:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.10_model.r WARNING @ Tue, 30 Jun 2020 02:21:23: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:21:23: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 30 Jun 2020 02:21:23: #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 02:21:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:21:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:21:24: 12000000 INFO @ Tue, 30 Jun 2020 02:21:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:21:29: 13000000 INFO @ Tue, 30 Jun 2020 02:21:34: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:21:39: 15000000 INFO @ Tue, 30 Jun 2020 02:21:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:21:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:21:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.05_summits.bed INFO @ Tue, 30 Jun 2020 02:21:44: Done! pass1 - making usageList (737 chroms): 3 millis pass2 - checking and writing primary data (15160 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:21:45: 16000000 INFO @ Tue, 30 Jun 2020 02:21:50: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:21:50: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:21:50: #1 total tags in treatment: 16962596 INFO @ Tue, 30 Jun 2020 02:21:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:21:50: #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 02:21:51: #1 tags after filtering in treatment: 16962505 INFO @ Tue, 30 Jun 2020 02:21:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:21:51: #1 finished! INFO @ Tue, 30 Jun 2020 02:21:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:21:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:21:52: #2 number of paired peaks: 217 WARNING @ Tue, 30 Jun 2020 02:21:52: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Tue, 30 Jun 2020 02:21:52: start model_add_line... INFO @ Tue, 30 Jun 2020 02:21:52: start X-correlation... INFO @ Tue, 30 Jun 2020 02:21:52: end of X-cor INFO @ Tue, 30 Jun 2020 02:21:52: #2 finished! INFO @ Tue, 30 Jun 2020 02:21:52: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:21:52: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 30 Jun 2020 02:21:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.20_model.r WARNING @ Tue, 30 Jun 2020 02:21:52: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:21:52: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 30 Jun 2020 02:21:52: #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 02:21:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:21:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:21:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:22:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:22:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:22:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.10_summits.bed INFO @ Tue, 30 Jun 2020 02:22:15: Done! pass1 - making usageList (504 chroms): 2 millis pass2 - checking and writing primary data (8779 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:22:27: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:22:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:22:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592424/SRX2592424.20_summits.bed INFO @ Tue, 30 Jun 2020 02:22:43: Done! pass1 - making usageList (217 chroms): 1 millis pass2 - checking and writing primary data (1197 records, 4 fields): 8 millis CompletedMACS2peakCalling