Job ID = 6627556 SRX = SRX8521352 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: 00:11:14 59776907 reads; of these: 59776907 (100.00%) were unpaired; of these: 43165982 (72.21%) aligned 0 times 11109266 (18.58%) aligned exactly 1 time 5501659 (9.20%) aligned >1 times 27.79% overall alignment rate Time searching: 00:11:14 Overall time: 00:11:14 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 8 files... [bam_rmdupse_core] 4651894 / 16610925 = 0.2801 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 12:13:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.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 12:13:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:13:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:14:04: 1000000 INFO @ Tue, 14 Jul 2020 12:14:09: 2000000 INFO @ Tue, 14 Jul 2020 12:14:14: 3000000 INFO @ Tue, 14 Jul 2020 12:14:20: 4000000 INFO @ Tue, 14 Jul 2020 12:14:25: 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, 14 Jul 2020 12:14:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.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 12:14:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:14:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:14:30: 6000000 INFO @ Tue, 14 Jul 2020 12:14:33: 1000000 INFO @ Tue, 14 Jul 2020 12:14:36: 7000000 INFO @ Tue, 14 Jul 2020 12:14:39: 2000000 INFO @ Tue, 14 Jul 2020 12:14:41: 8000000 INFO @ Tue, 14 Jul 2020 12:14:44: 3000000 INFO @ Tue, 14 Jul 2020 12:14:47: 9000000 INFO @ Tue, 14 Jul 2020 12:14:50: 4000000 INFO @ Tue, 14 Jul 2020 12:14:52: 10000000 INFO @ Tue, 14 Jul 2020 12:14:55: 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, 14 Jul 2020 12:14:58: 11000000 INFO @ Tue, 14 Jul 2020 12:14:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.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 12:14:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:14:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:15:01: 6000000 INFO @ Tue, 14 Jul 2020 12:15:03: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 12:15:03: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 12:15:03: #1 total tags in treatment: 11959031 INFO @ Tue, 14 Jul 2020 12:15:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:15:03: #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 12:15:03: 1000000 INFO @ Tue, 14 Jul 2020 12:15:04: #1 tags after filtering in treatment: 11958907 INFO @ Tue, 14 Jul 2020 12:15:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:15:04: #1 finished! INFO @ Tue, 14 Jul 2020 12:15:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:15:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:15:04: #2 number of paired peaks: 338 WARNING @ Tue, 14 Jul 2020 12:15:04: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 14 Jul 2020 12:15:04: start model_add_line... INFO @ Tue, 14 Jul 2020 12:15:05: start X-correlation... INFO @ Tue, 14 Jul 2020 12:15:05: end of X-cor INFO @ Tue, 14 Jul 2020 12:15:05: #2 finished! INFO @ Tue, 14 Jul 2020 12:15:05: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:15:05: #2 alternative fragment length(s) may be 4,59,598 bps INFO @ Tue, 14 Jul 2020 12:15:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.05_model.r WARNING @ Tue, 14 Jul 2020 12:15:05: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:15:05: #2 You may need to consider one of the other alternative d(s): 4,59,598 WARNING @ Tue, 14 Jul 2020 12:15:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:15:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:15:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:15:06: 7000000 INFO @ Tue, 14 Jul 2020 12:15:09: 2000000 INFO @ Tue, 14 Jul 2020 12:15:12: 8000000 INFO @ Tue, 14 Jul 2020 12:15:14: 3000000 INFO @ Tue, 14 Jul 2020 12:15:17: 9000000 INFO @ Tue, 14 Jul 2020 12:15:20: 4000000 INFO @ Tue, 14 Jul 2020 12:15:22: 10000000 INFO @ Tue, 14 Jul 2020 12:15:25: 5000000 INFO @ Tue, 14 Jul 2020 12:15:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:15:28: 11000000 INFO @ Tue, 14 Jul 2020 12:15:31: 6000000 INFO @ Tue, 14 Jul 2020 12:15:34: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 12:15:34: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 12:15:34: #1 total tags in treatment: 11959031 INFO @ Tue, 14 Jul 2020 12:15:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:15:34: #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 12:15:34: #1 tags after filtering in treatment: 11958907 INFO @ Tue, 14 Jul 2020 12:15:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:15:34: #1 finished! INFO @ Tue, 14 Jul 2020 12:15:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:15:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:15:35: #2 number of paired peaks: 338 WARNING @ Tue, 14 Jul 2020 12:15:35: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 14 Jul 2020 12:15:35: start model_add_line... INFO @ Tue, 14 Jul 2020 12:15:35: start X-correlation... INFO @ Tue, 14 Jul 2020 12:15:35: end of X-cor INFO @ Tue, 14 Jul 2020 12:15:35: #2 finished! INFO @ Tue, 14 Jul 2020 12:15:35: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:15:35: #2 alternative fragment length(s) may be 4,59,598 bps INFO @ Tue, 14 Jul 2020 12:15:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.10_model.r WARNING @ Tue, 14 Jul 2020 12:15:35: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:15:35: #2 You may need to consider one of the other alternative d(s): 4,59,598 WARNING @ Tue, 14 Jul 2020 12:15:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:15:35: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:15:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:15:36: 7000000 INFO @ Tue, 14 Jul 2020 12:15:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:15:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:15:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.05_summits.bed INFO @ Tue, 14 Jul 2020 12:15:39: Done! pass1 - making usageList (410 chroms): 1 millis pass2 - checking and writing primary data (1781 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:15:41: 8000000 INFO @ Tue, 14 Jul 2020 12:15:47: 9000000 INFO @ Tue, 14 Jul 2020 12:15:52: 10000000 INFO @ Tue, 14 Jul 2020 12:15:57: 11000000 INFO @ Tue, 14 Jul 2020 12:15:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:16:03: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 12:16:03: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 12:16:03: #1 total tags in treatment: 11959031 INFO @ Tue, 14 Jul 2020 12:16:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:16:03: #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 12:16:03: #1 tags after filtering in treatment: 11958907 INFO @ Tue, 14 Jul 2020 12:16:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:16:03: #1 finished! INFO @ Tue, 14 Jul 2020 12:16:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:16:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:16:04: #2 number of paired peaks: 338 WARNING @ Tue, 14 Jul 2020 12:16:04: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 14 Jul 2020 12:16:04: start model_add_line... INFO @ Tue, 14 Jul 2020 12:16:04: start X-correlation... INFO @ Tue, 14 Jul 2020 12:16:04: end of X-cor INFO @ Tue, 14 Jul 2020 12:16:04: #2 finished! INFO @ Tue, 14 Jul 2020 12:16:04: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:16:04: #2 alternative fragment length(s) may be 4,59,598 bps INFO @ Tue, 14 Jul 2020 12:16:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.20_model.r WARNING @ Tue, 14 Jul 2020 12:16:04: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:16:04: #2 You may need to consider one of the other alternative d(s): 4,59,598 WARNING @ Tue, 14 Jul 2020 12:16:04: #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 12:16:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:16:04: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:16:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:16:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:16:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.10_summits.bed INFO @ Tue, 14 Jul 2020 12:16:10: Done! pass1 - making usageList (260 chroms): 1 millis pass2 - checking and writing primary data (663 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:16:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:16:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:16:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:16:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521352/SRX8521352.20_summits.bed INFO @ Tue, 14 Jul 2020 12:16:39: Done! pass1 - making usageList (103 chroms): 1 millis pass2 - checking and writing primary data (229 records, 4 fields): 3 millis CompletedMACS2peakCalling