Job ID = 6529872 SRX = SRX5343134 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: 00:04:32 14324589 reads; of these: 14324589 (100.00%) were unpaired; of these: 1397805 (9.76%) aligned 0 times 11011477 (76.87%) aligned exactly 1 time 1915307 (13.37%) aligned >1 times 90.24% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 1839721 / 12926784 = 0.1423 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 03:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.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 03:10:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:40: 1000000 INFO @ Tue, 30 Jun 2020 03:10:47: 2000000 INFO @ Tue, 30 Jun 2020 03:10:53: 3000000 INFO @ Tue, 30 Jun 2020 03:11:00: 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 03:11:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.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 03:11:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:11:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:11:06: 5000000 INFO @ Tue, 30 Jun 2020 03:11:11: 1000000 INFO @ Tue, 30 Jun 2020 03:11:13: 6000000 INFO @ Tue, 30 Jun 2020 03:11:18: 2000000 INFO @ Tue, 30 Jun 2020 03:11:20: 7000000 INFO @ Tue, 30 Jun 2020 03:11:26: 3000000 INFO @ Tue, 30 Jun 2020 03:11:27: 8000000 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 03:11:33: 4000000 INFO @ Tue, 30 Jun 2020 03:11:34: 9000000 INFO @ Tue, 30 Jun 2020 03:11:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.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 03:11:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:11:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:11:40: 5000000 INFO @ Tue, 30 Jun 2020 03:11:41: 1000000 INFO @ Tue, 30 Jun 2020 03:11:41: 10000000 INFO @ Tue, 30 Jun 2020 03:11:47: 6000000 INFO @ Tue, 30 Jun 2020 03:11:47: 2000000 INFO @ Tue, 30 Jun 2020 03:11:48: 11000000 INFO @ Tue, 30 Jun 2020 03:11:48: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:11:48: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:11:48: #1 total tags in treatment: 11087063 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: 11087057 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 03:11:50: #2 number of paired peaks: 170 WARNING @ Tue, 30 Jun 2020 03:11:50: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:50: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:50: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:50: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:50: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:50: #2 predicted fragment length is 67 bps INFO @ Tue, 30 Jun 2020 03:11:50: #2 alternative fragment length(s) may be 67 bps INFO @ Tue, 30 Jun 2020 03:11:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.05_model.r WARNING @ Tue, 30 Jun 2020 03:11:50: #2 Since the d (67) 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): 67 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 03:11:53: 3000000 INFO @ Tue, 30 Jun 2020 03:11:54: 7000000 INFO @ Tue, 30 Jun 2020 03:11:59: 4000000 INFO @ Tue, 30 Jun 2020 03:12:00: 8000000 INFO @ Tue, 30 Jun 2020 03:12:06: 5000000 INFO @ Tue, 30 Jun 2020 03:12:06: 9000000 INFO @ Tue, 30 Jun 2020 03:12:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:12: 6000000 INFO @ Tue, 30 Jun 2020 03:12:13: 10000000 INFO @ Tue, 30 Jun 2020 03:12:18: 7000000 INFO @ Tue, 30 Jun 2020 03:12:19: 11000000 INFO @ Tue, 30 Jun 2020 03:12:20: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:12:20: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:12:20: #1 total tags in treatment: 11087063 INFO @ Tue, 30 Jun 2020 03:12:20: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:20: #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 03:12:20: #1 tags after filtering in treatment: 11087057 INFO @ Tue, 30 Jun 2020 03:12:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:20: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:21: #2 number of paired peaks: 170 WARNING @ Tue, 30 Jun 2020 03:12:21: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:21: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:21: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:21: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:21: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:21: #2 predicted fragment length is 67 bps INFO @ Tue, 30 Jun 2020 03:12:21: #2 alternative fragment length(s) may be 67 bps INFO @ Tue, 30 Jun 2020 03:12:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.10_model.r WARNING @ Tue, 30 Jun 2020 03:12:21: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:21: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Tue, 30 Jun 2020 03:12:21: #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 03:12:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.05_summits.bed INFO @ Tue, 30 Jun 2020 03:12:22: Done! pass1 - making usageList (259 chroms): 1 millis pass2 - checking and writing primary data (696 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:12:24: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:12:30: 9000000 INFO @ Tue, 30 Jun 2020 03:12:35: 10000000 INFO @ Tue, 30 Jun 2020 03:12:41: 11000000 INFO @ Tue, 30 Jun 2020 03:12:41: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:12:41: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:12:41: #1 total tags in treatment: 11087063 INFO @ Tue, 30 Jun 2020 03:12:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:41: #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 03:12:42: #1 tags after filtering in treatment: 11087057 INFO @ Tue, 30 Jun 2020 03:12:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:42: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:42: #2 number of paired peaks: 170 WARNING @ Tue, 30 Jun 2020 03:12:42: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:42: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:42: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:43: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:43: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:43: #2 predicted fragment length is 67 bps INFO @ Tue, 30 Jun 2020 03:12:43: #2 alternative fragment length(s) may be 67 bps INFO @ Tue, 30 Jun 2020 03:12:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.20_model.r WARNING @ Tue, 30 Jun 2020 03:12:43: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:43: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Tue, 30 Jun 2020 03:12:43: #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 03:12:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:12:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.10_summits.bed INFO @ Tue, 30 Jun 2020 03:12:53: Done! pass1 - making usageList (148 chroms): 2 millis pass2 - checking and writing primary data (324 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:13:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343134/SRX5343134.20_summits.bed INFO @ Tue, 30 Jun 2020 03:13:15: Done! pass1 - making usageList (93 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 4 millis CompletedMACS2peakCalling