Job ID = 6529729 SRX = SRX4510349 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: 00:00:01 Multiseed full-index search: 00:10:38 24091206 reads; of these: 24091206 (100.00%) were unpaired; of these: 2448454 (10.16%) aligned 0 times 19005963 (78.89%) aligned exactly 1 time 2636789 (10.95%) aligned >1 times 89.84% overall alignment rate Time searching: 00:10:39 Overall time: 00:10:39 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] 3860778 / 21642752 = 0.1784 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 02:44:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.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 02:44:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:44:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:44:32: 1000000 INFO @ Tue, 30 Jun 2020 02:44:41: 2000000 INFO @ Tue, 30 Jun 2020 02:44:49: 3000000 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 02:44:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.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 02:44:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:44:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:44:59: 4000000 INFO @ Tue, 30 Jun 2020 02:45:04: 1000000 INFO @ Tue, 30 Jun 2020 02:45:09: 5000000 INFO @ Tue, 30 Jun 2020 02:45:14: 2000000 INFO @ Tue, 30 Jun 2020 02:45:20: 6000000 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 02:45:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.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 02:45:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:24: 3000000 INFO @ Tue, 30 Jun 2020 02:45:31: 7000000 INFO @ Tue, 30 Jun 2020 02:45:35: 1000000 INFO @ Tue, 30 Jun 2020 02:45:35: 4000000 INFO @ Tue, 30 Jun 2020 02:45:44: 8000000 INFO @ Tue, 30 Jun 2020 02:45:47: 2000000 INFO @ Tue, 30 Jun 2020 02:45:47: 5000000 INFO @ Tue, 30 Jun 2020 02:45:56: 9000000 INFO @ Tue, 30 Jun 2020 02:45:58: 3000000 INFO @ Tue, 30 Jun 2020 02:45:59: 6000000 INFO @ Tue, 30 Jun 2020 02:46:08: 10000000 INFO @ Tue, 30 Jun 2020 02:46:10: 4000000 INFO @ Tue, 30 Jun 2020 02:46:12: 7000000 INFO @ Tue, 30 Jun 2020 02:46:20: 11000000 INFO @ Tue, 30 Jun 2020 02:46:22: 5000000 INFO @ Tue, 30 Jun 2020 02:46:24: 8000000 INFO @ Tue, 30 Jun 2020 02:46:32: 12000000 INFO @ Tue, 30 Jun 2020 02:46:34: 6000000 INFO @ Tue, 30 Jun 2020 02:46:36: 9000000 INFO @ Tue, 30 Jun 2020 02:46:45: 13000000 INFO @ Tue, 30 Jun 2020 02:46:47: 7000000 INFO @ Tue, 30 Jun 2020 02:46:49: 10000000 INFO @ Tue, 30 Jun 2020 02:46:58: 14000000 INFO @ Tue, 30 Jun 2020 02:46:59: 8000000 INFO @ Tue, 30 Jun 2020 02:47:01: 11000000 INFO @ Tue, 30 Jun 2020 02:47:11: 15000000 INFO @ Tue, 30 Jun 2020 02:47:11: 9000000 INFO @ Tue, 30 Jun 2020 02:47:13: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:47:24: 16000000 INFO @ Tue, 30 Jun 2020 02:47:25: 10000000 INFO @ Tue, 30 Jun 2020 02:47:26: 13000000 INFO @ Tue, 30 Jun 2020 02:47:37: 17000000 INFO @ Tue, 30 Jun 2020 02:47:38: 14000000 INFO @ Tue, 30 Jun 2020 02:47:39: 11000000 INFO @ Tue, 30 Jun 2020 02:47:48: #1 tag size is determined as 101 bps INFO @ Tue, 30 Jun 2020 02:47:48: #1 tag size = 101 INFO @ Tue, 30 Jun 2020 02:47:48: #1 total tags in treatment: 17781974 INFO @ Tue, 30 Jun 2020 02:47:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:47:48: #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 02:47:49: #1 tags after filtering in treatment: 17781796 INFO @ Tue, 30 Jun 2020 02:47:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:47:49: #1 finished! INFO @ Tue, 30 Jun 2020 02:47:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:47:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:47:50: #2 number of paired peaks: 152 WARNING @ Tue, 30 Jun 2020 02:47:50: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 30 Jun 2020 02:47:50: start model_add_line... INFO @ Tue, 30 Jun 2020 02:47:50: start X-correlation... INFO @ Tue, 30 Jun 2020 02:47:50: end of X-cor INFO @ Tue, 30 Jun 2020 02:47:50: #2 finished! INFO @ Tue, 30 Jun 2020 02:47:50: #2 predicted fragment length is 102 bps INFO @ Tue, 30 Jun 2020 02:47:50: #2 alternative fragment length(s) may be 2,102,593 bps INFO @ Tue, 30 Jun 2020 02:47:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.05_model.r WARNING @ Tue, 30 Jun 2020 02:47:50: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:47:50: #2 You may need to consider one of the other alternative d(s): 2,102,593 WARNING @ Tue, 30 Jun 2020 02:47:50: #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 02:47:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:47:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:47:52: 15000000 INFO @ Tue, 30 Jun 2020 02:47:53: 12000000 INFO @ Tue, 30 Jun 2020 02:48:05: 16000000 INFO @ Tue, 30 Jun 2020 02:48:06: 13000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:48:18: 17000000 INFO @ Tue, 30 Jun 2020 02:48:19: 14000000 INFO @ Tue, 30 Jun 2020 02:48:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:48:29: #1 tag size is determined as 101 bps INFO @ Tue, 30 Jun 2020 02:48:29: #1 tag size = 101 INFO @ Tue, 30 Jun 2020 02:48:29: #1 total tags in treatment: 17781974 INFO @ Tue, 30 Jun 2020 02:48:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:29: #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 02:48:29: #1 tags after filtering in treatment: 17781796 INFO @ Tue, 30 Jun 2020 02:48:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:29: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:31: #2 number of paired peaks: 152 WARNING @ Tue, 30 Jun 2020 02:48:31: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:31: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:31: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:31: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:31: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:31: #2 predicted fragment length is 102 bps INFO @ Tue, 30 Jun 2020 02:48:31: #2 alternative fragment length(s) may be 2,102,593 bps INFO @ Tue, 30 Jun 2020 02:48:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.10_model.r WARNING @ Tue, 30 Jun 2020 02:48:31: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:48:31: #2 You may need to consider one of the other alternative d(s): 2,102,593 WARNING @ Tue, 30 Jun 2020 02:48:31: #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 02:48:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:48:33: 15000000 INFO @ Tue, 30 Jun 2020 02:48:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:48:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:48:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.05_summits.bed INFO @ Tue, 30 Jun 2020 02:48:45: Done! pass1 - making usageList (395 chroms): 2 millis pass2 - checking and writing primary data (5402 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:48:45: 16000000 INFO @ Tue, 30 Jun 2020 02:48:58: 17000000 INFO @ Tue, 30 Jun 2020 02:49:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:49:08: #1 tag size is determined as 101 bps INFO @ Tue, 30 Jun 2020 02:49:08: #1 tag size = 101 INFO @ Tue, 30 Jun 2020 02:49:08: #1 total tags in treatment: 17781974 INFO @ Tue, 30 Jun 2020 02:49:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:08: #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 02:49:09: #1 tags after filtering in treatment: 17781796 INFO @ Tue, 30 Jun 2020 02:49:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:49:09: #1 finished! INFO @ Tue, 30 Jun 2020 02:49:09: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:49:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:49:10: #2 number of paired peaks: 152 WARNING @ Tue, 30 Jun 2020 02:49:10: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 30 Jun 2020 02:49:10: start model_add_line... INFO @ Tue, 30 Jun 2020 02:49:10: start X-correlation... INFO @ Tue, 30 Jun 2020 02:49:10: end of X-cor INFO @ Tue, 30 Jun 2020 02:49:10: #2 finished! INFO @ Tue, 30 Jun 2020 02:49:10: #2 predicted fragment length is 102 bps INFO @ Tue, 30 Jun 2020 02:49:10: #2 alternative fragment length(s) may be 2,102,593 bps INFO @ Tue, 30 Jun 2020 02:49:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.20_model.r WARNING @ Tue, 30 Jun 2020 02:49:10: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:49:10: #2 You may need to consider one of the other alternative d(s): 2,102,593 WARNING @ Tue, 30 Jun 2020 02:49:10: #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 02:49:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:49:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:49:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:49:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:49:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.10_summits.bed INFO @ Tue, 30 Jun 2020 02:49:23: Done! pass1 - making usageList (309 chroms): 1 millis pass2 - checking and writing primary data (1825 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:49:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4510349/SRX4510349.20_summits.bed INFO @ Tue, 30 Jun 2020 02:50:02: Done! pass1 - making usageList (197 chroms): 2 millis pass2 - checking and writing primary data (411 records, 4 fields): 12 millis CompletedMACS2peakCalling