Job ID = 6529750 SRX = SRX4669057 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: 00:05:13 22469588 reads; of these: 22469588 (100.00%) were unpaired; of these: 1181480 (5.26%) aligned 0 times 18651508 (83.01%) aligned exactly 1 time 2636600 (11.73%) aligned >1 times 94.74% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 4571320 / 21288108 = 0.2147 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 02:45:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.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 02:45:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:35: 1000000 INFO @ Tue, 30 Jun 2020 02:45:41: 2000000 INFO @ Tue, 30 Jun 2020 02:45:47: 3000000 INFO @ Tue, 30 Jun 2020 02:45:53: 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 02:45:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.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 02:45:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:00: 5000000 INFO @ Tue, 30 Jun 2020 02:46:06: 1000000 INFO @ Tue, 30 Jun 2020 02:46:06: 6000000 INFO @ Tue, 30 Jun 2020 02:46:13: 2000000 INFO @ Tue, 30 Jun 2020 02:46:13: 7000000 INFO @ Tue, 30 Jun 2020 02:46:19: 3000000 INFO @ Tue, 30 Jun 2020 02:46:20: 8000000 INFO @ Tue, 30 Jun 2020 02:46:26: 4000000 INFO @ Tue, 30 Jun 2020 02:46:27: 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 02:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.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 02:46:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:33: 5000000 INFO @ Tue, 30 Jun 2020 02:46:33: 10000000 INFO @ Tue, 30 Jun 2020 02:46:36: 1000000 INFO @ Tue, 30 Jun 2020 02:46:39: 6000000 INFO @ Tue, 30 Jun 2020 02:46:40: 11000000 INFO @ Tue, 30 Jun 2020 02:46:42: 2000000 INFO @ Tue, 30 Jun 2020 02:46:46: 7000000 INFO @ Tue, 30 Jun 2020 02:46:47: 12000000 INFO @ Tue, 30 Jun 2020 02:46:49: 3000000 INFO @ Tue, 30 Jun 2020 02:46:53: 8000000 INFO @ Tue, 30 Jun 2020 02:46:53: 13000000 INFO @ Tue, 30 Jun 2020 02:46:55: 4000000 INFO @ Tue, 30 Jun 2020 02:46:59: 9000000 INFO @ Tue, 30 Jun 2020 02:47:00: 14000000 INFO @ Tue, 30 Jun 2020 02:47:01: 5000000 INFO @ Tue, 30 Jun 2020 02:47:06: 10000000 INFO @ Tue, 30 Jun 2020 02:47:07: 15000000 INFO @ Tue, 30 Jun 2020 02:47:08: 6000000 INFO @ Tue, 30 Jun 2020 02:47:13: 11000000 INFO @ Tue, 30 Jun 2020 02:47:14: 16000000 INFO @ Tue, 30 Jun 2020 02:47:14: 7000000 INFO @ Tue, 30 Jun 2020 02:47:19: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:47:19: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:47:19: #1 total tags in treatment: 16716788 INFO @ Tue, 30 Jun 2020 02:47:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:47:19: #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 02:47:20: 12000000 INFO @ Tue, 30 Jun 2020 02:47:20: #1 tags after filtering in treatment: 16716754 INFO @ Tue, 30 Jun 2020 02:47:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:47:20: #1 finished! INFO @ Tue, 30 Jun 2020 02:47:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:47:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:47:20: 8000000 INFO @ Tue, 30 Jun 2020 02:47:21: #2 number of paired peaks: 115 WARNING @ Tue, 30 Jun 2020 02:47:21: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 30 Jun 2020 02:47:21: start model_add_line... INFO @ Tue, 30 Jun 2020 02:47:21: start X-correlation... INFO @ Tue, 30 Jun 2020 02:47:21: end of X-cor INFO @ Tue, 30 Jun 2020 02:47:21: #2 finished! INFO @ Tue, 30 Jun 2020 02:47:21: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:47:21: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 02:47:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.05_model.r WARNING @ Tue, 30 Jun 2020 02:47:21: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:47:21: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 02:47:21: #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 02:47:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:47:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:47:26: 13000000 INFO @ Tue, 30 Jun 2020 02:47:27: 9000000 INFO @ Tue, 30 Jun 2020 02:47:33: 10000000 INFO @ Tue, 30 Jun 2020 02:47:34: 14000000 INFO @ Tue, 30 Jun 2020 02:47:39: 11000000 INFO @ Tue, 30 Jun 2020 02:47:41: 15000000 INFO @ Tue, 30 Jun 2020 02:47:45: 12000000 INFO @ Tue, 30 Jun 2020 02:47:48: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:47:52: 13000000 INFO @ Tue, 30 Jun 2020 02:47:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:47:53: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:47:53: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:47:53: #1 total tags in treatment: 16716788 INFO @ Tue, 30 Jun 2020 02:47:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:47:53: #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 02:47:54: #1 tags after filtering in treatment: 16716754 INFO @ Tue, 30 Jun 2020 02:47:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:47:54: #1 finished! INFO @ Tue, 30 Jun 2020 02:47:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:47:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:47:55: #2 number of paired peaks: 115 WARNING @ Tue, 30 Jun 2020 02:47:55: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 30 Jun 2020 02:47:55: start model_add_line... INFO @ Tue, 30 Jun 2020 02:47:55: start X-correlation... INFO @ Tue, 30 Jun 2020 02:47:55: end of X-cor INFO @ Tue, 30 Jun 2020 02:47:55: #2 finished! INFO @ Tue, 30 Jun 2020 02:47:55: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:47:55: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 02:47:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.10_model.r WARNING @ Tue, 30 Jun 2020 02:47:55: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:47:55: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 02:47:55: #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 02:47:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:47:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:47:58: 14000000 INFO @ Tue, 30 Jun 2020 02:48:03: 15000000 INFO @ Tue, 30 Jun 2020 02:48:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:48:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:48:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.05_summits.bed INFO @ Tue, 30 Jun 2020 02:48:08: Done! INFO @ Tue, 30 Jun 2020 02:48:08: 16000000 pass1 - making usageList (427 chroms): 1 millis pass2 - checking and writing primary data (2324 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:48:12: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:48:12: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:48:12: #1 total tags in treatment: 16716788 INFO @ Tue, 30 Jun 2020 02:48:12: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:12: #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 02:48:13: #1 tags after filtering in treatment: 16716754 INFO @ Tue, 30 Jun 2020 02:48:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:13: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:13: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:14: #2 number of paired peaks: 115 WARNING @ Tue, 30 Jun 2020 02:48:14: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:14: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:14: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:14: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:14: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:14: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:48:14: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 02:48:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.20_model.r WARNING @ Tue, 30 Jun 2020 02:48:14: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:48:14: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 02:48:14: #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 02:48:14: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:48:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:48:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:48:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:48:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.10_summits.bed INFO @ Tue, 30 Jun 2020 02:48:41: Done! pass1 - making usageList (275 chroms): 1 millis pass2 - checking and writing primary data (589 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:48:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:49:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:49:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:49:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669057/SRX4669057.20_summits.bed INFO @ Tue, 30 Jun 2020 02:49:01: Done! pass1 - making usageList (92 chroms): 1 millis pass2 - checking and writing primary data (174 records, 4 fields): 4 millis CompletedMACS2peakCalling