Job ID = 6627557 SRX = SRX8521347 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: 00:11:44 69027235 reads; of these: 69027235 (100.00%) were unpaired; of these: 56684567 (82.12%) aligned 0 times 7916309 (11.47%) aligned exactly 1 time 4426359 (6.41%) aligned >1 times 17.88% overall alignment rate Time searching: 00:11:44 Overall time: 00:11:44 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] 3324886 / 12342668 = 0.2694 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, 14 Jul 2020 12:13:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.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, 14 Jul 2020 12:13:42: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:13:42: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:13:48: 1000000 INFO @ Tue, 14 Jul 2020 12:13:53: 2000000 INFO @ Tue, 14 Jul 2020 12:13:58: 3000000 INFO @ Tue, 14 Jul 2020 12:14:03: 4000000 INFO @ Tue, 14 Jul 2020 12:14:08: 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, 14 Jul 2020 12:14:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.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, 14 Jul 2020 12:14:12: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:14:12: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:14:13: 6000000 INFO @ Tue, 14 Jul 2020 12:14:17: 1000000 INFO @ Tue, 14 Jul 2020 12:14:18: 7000000 INFO @ Tue, 14 Jul 2020 12:14:22: 2000000 INFO @ Tue, 14 Jul 2020 12:14:23: 8000000 INFO @ Tue, 14 Jul 2020 12:14:27: 3000000 INFO @ Tue, 14 Jul 2020 12:14:28: 9000000 INFO @ Tue, 14 Jul 2020 12:14:28: #1 tag size is determined as 71 bps INFO @ Tue, 14 Jul 2020 12:14:28: #1 tag size = 71 INFO @ Tue, 14 Jul 2020 12:14:28: #1 total tags in treatment: 9017782 INFO @ Tue, 14 Jul 2020 12:14:28: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:14:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:14:29: #1 tags after filtering in treatment: 9017644 INFO @ Tue, 14 Jul 2020 12:14:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:14:29: #1 finished! INFO @ Tue, 14 Jul 2020 12:14:29: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:14:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:14:29: #2 number of paired peaks: 413 WARNING @ Tue, 14 Jul 2020 12:14:29: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Tue, 14 Jul 2020 12:14:29: start model_add_line... INFO @ Tue, 14 Jul 2020 12:14:29: start X-correlation... INFO @ Tue, 14 Jul 2020 12:14:30: end of X-cor INFO @ Tue, 14 Jul 2020 12:14:30: #2 finished! INFO @ Tue, 14 Jul 2020 12:14:30: #2 predicted fragment length is 55 bps INFO @ Tue, 14 Jul 2020 12:14:30: #2 alternative fragment length(s) may be 4,55 bps INFO @ Tue, 14 Jul 2020 12:14:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.05_model.r WARNING @ Tue, 14 Jul 2020 12:14:30: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:14:30: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Tue, 14 Jul 2020 12:14:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:14:30: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:14:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:14:32: 4000000 INFO @ Tue, 14 Jul 2020 12:14:37: 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, 14 Jul 2020 12:14:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.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, 14 Jul 2020 12:14:42: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:14:42: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:14:42: 6000000 INFO @ Tue, 14 Jul 2020 12:14:47: 7000000 INFO @ Tue, 14 Jul 2020 12:14:48: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:14:48: 1000000 INFO @ Tue, 14 Jul 2020 12:14:53: 8000000 INFO @ Tue, 14 Jul 2020 12:14:54: 2000000 INFO @ Tue, 14 Jul 2020 12:14:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:14:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:14:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.05_summits.bed INFO @ Tue, 14 Jul 2020 12:14:57: Done! pass1 - making usageList (335 chroms): 1 millis pass2 - checking and writing primary data (960 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:14:58: 9000000 INFO @ Tue, 14 Jul 2020 12:14:58: #1 tag size is determined as 71 bps INFO @ Tue, 14 Jul 2020 12:14:58: #1 tag size = 71 INFO @ Tue, 14 Jul 2020 12:14:58: #1 total tags in treatment: 9017782 INFO @ Tue, 14 Jul 2020 12:14:58: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:14:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:14:59: #1 tags after filtering in treatment: 9017644 INFO @ Tue, 14 Jul 2020 12:14:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:14:59: #1 finished! INFO @ Tue, 14 Jul 2020 12:14:59: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:14:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:14:59: #2 number of paired peaks: 413 WARNING @ Tue, 14 Jul 2020 12:14:59: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Tue, 14 Jul 2020 12:14:59: start model_add_line... INFO @ Tue, 14 Jul 2020 12:14:59: start X-correlation... INFO @ Tue, 14 Jul 2020 12:14:59: end of X-cor INFO @ Tue, 14 Jul 2020 12:14:59: #2 finished! INFO @ Tue, 14 Jul 2020 12:14:59: #2 predicted fragment length is 55 bps INFO @ Tue, 14 Jul 2020 12:14:59: #2 alternative fragment length(s) may be 4,55 bps INFO @ Tue, 14 Jul 2020 12:14:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.10_model.r WARNING @ Tue, 14 Jul 2020 12:14:59: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:14:59: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Tue, 14 Jul 2020 12:14:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:14:59: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:14:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:15:00: 3000000 INFO @ Tue, 14 Jul 2020 12:15:06: 4000000 INFO @ Tue, 14 Jul 2020 12:15:12: 5000000 INFO @ Tue, 14 Jul 2020 12:15:17: 6000000 INFO @ Tue, 14 Jul 2020 12:15:18: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:15:23: 7000000 INFO @ Tue, 14 Jul 2020 12:15:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:15:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:15:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.10_summits.bed INFO @ Tue, 14 Jul 2020 12:15:26: Done! pass1 - making usageList (160 chroms): 0 millis pass2 - checking and writing primary data (402 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:15:29: 8000000 INFO @ Tue, 14 Jul 2020 12:15:35: 9000000 INFO @ Tue, 14 Jul 2020 12:15:35: #1 tag size is determined as 71 bps INFO @ Tue, 14 Jul 2020 12:15:35: #1 tag size = 71 INFO @ Tue, 14 Jul 2020 12:15:35: #1 total tags in treatment: 9017782 INFO @ Tue, 14 Jul 2020 12:15:35: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:15:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:15:36: #1 tags after filtering in treatment: 9017644 INFO @ Tue, 14 Jul 2020 12:15:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:15:36: #1 finished! INFO @ Tue, 14 Jul 2020 12:15:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:15:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:15:36: #2 number of paired peaks: 413 WARNING @ Tue, 14 Jul 2020 12:15:36: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Tue, 14 Jul 2020 12:15:36: start model_add_line... INFO @ Tue, 14 Jul 2020 12:15:36: start X-correlation... INFO @ Tue, 14 Jul 2020 12:15:36: end of X-cor INFO @ Tue, 14 Jul 2020 12:15:36: #2 finished! INFO @ Tue, 14 Jul 2020 12:15:36: #2 predicted fragment length is 55 bps INFO @ Tue, 14 Jul 2020 12:15:36: #2 alternative fragment length(s) may be 4,55 bps INFO @ Tue, 14 Jul 2020 12:15:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.20_model.r WARNING @ Tue, 14 Jul 2020 12:15:36: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:15:36: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Tue, 14 Jul 2020 12:15:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:15:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:15:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:15:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521347/SRX8521347.20_summits.bed INFO @ Tue, 14 Jul 2020 12:16:03: Done! pass1 - making usageList (93 chroms): 1 millis pass2 - checking and writing primary data (175 records, 4 fields): 3 millis CompletedMACS2peakCalling