Job ID = 6530045 SRX = SRX647917 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: 00:03:17 13124734 reads; of these: 13124734 (100.00%) were unpaired; of these: 960495 (7.32%) aligned 0 times 9960185 (75.89%) aligned exactly 1 time 2204054 (16.79%) aligned >1 times 92.68% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 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] 2472257 / 12164239 = 0.2032 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 03:10:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.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 03:10:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:11: 1000000 INFO @ Tue, 30 Jun 2020 03:10:17: 2000000 INFO @ Tue, 30 Jun 2020 03:10:23: 3000000 INFO @ Tue, 30 Jun 2020 03:10:29: 4000000 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 03:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.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 03:10:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:35: 5000000 INFO @ Tue, 30 Jun 2020 03:10:41: 6000000 INFO @ Tue, 30 Jun 2020 03:10:42: 1000000 INFO @ Tue, 30 Jun 2020 03:10:47: 7000000 INFO @ Tue, 30 Jun 2020 03:10:49: 2000000 INFO @ Tue, 30 Jun 2020 03:10:54: 8000000 INFO @ Tue, 30 Jun 2020 03:10:57: 3000000 INFO @ Tue, 30 Jun 2020 03:11:00: 9000000 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 03:11:04: 4000000 INFO @ Tue, 30 Jun 2020 03:11:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.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 03:11:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:11:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:11:05: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:11:05: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:11:05: #1 total tags in treatment: 9691982 INFO @ Tue, 30 Jun 2020 03:11:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:05: #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 03:11:05: #1 tags after filtering in treatment: 9691973 INFO @ Tue, 30 Jun 2020 03:11:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:05: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:06: #2 number of paired peaks: 352 WARNING @ Tue, 30 Jun 2020 03:11:06: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:06: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:06: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:06: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:06: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:06: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 03:11:06: #2 alternative fragment length(s) may be 3,54,582 bps INFO @ Tue, 30 Jun 2020 03:11:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.05_model.r WARNING @ Tue, 30 Jun 2020 03:11:06: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:11:06: #2 You may need to consider one of the other alternative d(s): 3,54,582 WARNING @ Tue, 30 Jun 2020 03:11:06: #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 03:11:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:11:11: 5000000 INFO @ Tue, 30 Jun 2020 03:11:12: 1000000 INFO @ Tue, 30 Jun 2020 03:11:19: 6000000 INFO @ Tue, 30 Jun 2020 03:11:20: 2000000 INFO @ Tue, 30 Jun 2020 03:11:24: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:11:27: 7000000 INFO @ Tue, 30 Jun 2020 03:11:28: 3000000 INFO @ Tue, 30 Jun 2020 03:11:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:11:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:11:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.05_summits.bed INFO @ Tue, 30 Jun 2020 03:11:34: Done! pass1 - making usageList (462 chroms): 2 millis pass2 - checking and writing primary data (1493 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:11:35: 8000000 INFO @ Tue, 30 Jun 2020 03:11:35: 4000000 INFO @ Tue, 30 Jun 2020 03:11:42: 9000000 INFO @ Tue, 30 Jun 2020 03:11:43: 5000000 INFO @ Tue, 30 Jun 2020 03:11:48: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:11:48: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:11:48: #1 total tags in treatment: 9691982 INFO @ Tue, 30 Jun 2020 03:11:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:48: #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 03:11:49: #1 tags after filtering in treatment: 9691973 INFO @ Tue, 30 Jun 2020 03:11:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:49: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:49: #2 number of paired peaks: 352 WARNING @ Tue, 30 Jun 2020 03:11:49: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:49: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:49: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:49: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:49: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:49: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 03:11:49: #2 alternative fragment length(s) may be 3,54,582 bps INFO @ Tue, 30 Jun 2020 03:11:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.10_model.r WARNING @ Tue, 30 Jun 2020 03:11:50: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:11:50: #2 You may need to consider one of the other alternative d(s): 3,54,582 WARNING @ Tue, 30 Jun 2020 03:11:50: #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 03:11:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:11:50: 6000000 INFO @ Tue, 30 Jun 2020 03:11:57: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:12:05: 8000000 INFO @ Tue, 30 Jun 2020 03:12:08: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:11: 9000000 INFO @ Tue, 30 Jun 2020 03:12:17: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:12:17: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:12:17: #1 total tags in treatment: 9691982 INFO @ Tue, 30 Jun 2020 03:12:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:17: #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 03:12:18: #1 tags after filtering in treatment: 9691973 INFO @ Tue, 30 Jun 2020 03:12:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:18: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.10_summits.bed INFO @ Tue, 30 Jun 2020 03:12:18: Done! pass1 - making usageList (262 chroms): 1 millis pass2 - checking and writing primary data (561 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:12:18: #2 number of paired peaks: 352 WARNING @ Tue, 30 Jun 2020 03:12:18: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:18: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:18: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:18: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:18: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:18: #2 predicted fragment length is 54 bps INFO @ Tue, 30 Jun 2020 03:12:18: #2 alternative fragment length(s) may be 3,54,582 bps INFO @ Tue, 30 Jun 2020 03:12:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.20_model.r WARNING @ Tue, 30 Jun 2020 03:12:18: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:18: #2 You may need to consider one of the other alternative d(s): 3,54,582 WARNING @ Tue, 30 Jun 2020 03:12:18: #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 03:12:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:12:37: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX647917/SRX647917.20_summits.bed INFO @ Tue, 30 Jun 2020 03:12:46: Done! pass1 - making usageList (111 chroms): 1 millis pass2 - checking and writing primary data (222 records, 4 fields): 7 millis CompletedMACS2peakCalling