Job ID = 6529748 SRX = SRX4669053 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: 00:06:07 25329650 reads; of these: 25329650 (100.00%) were unpaired; of these: 1915482 (7.56%) aligned 0 times 20106514 (79.38%) aligned exactly 1 time 3307654 (13.06%) aligned >1 times 92.44% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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] 4561303 / 23414168 = 0.1948 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 02:55:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.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 02:55:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:55:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:55:57: 1000000 INFO @ Tue, 30 Jun 2020 02:56:03: 2000000 INFO @ Tue, 30 Jun 2020 02:56:10: 3000000 INFO @ Tue, 30 Jun 2020 02:56:16: 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 02:56:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.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 02:56:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:56:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:56:22: 5000000 INFO @ Tue, 30 Jun 2020 02:56:28: 6000000 INFO @ Tue, 30 Jun 2020 02:56:29: 1000000 INFO @ Tue, 30 Jun 2020 02:56:34: 7000000 INFO @ Tue, 30 Jun 2020 02:56:36: 2000000 INFO @ Tue, 30 Jun 2020 02:56:40: 8000000 INFO @ Tue, 30 Jun 2020 02:56:44: 3000000 INFO @ Tue, 30 Jun 2020 02:56:46: 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 02:56:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.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 02:56:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:56:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:56:52: 4000000 INFO @ Tue, 30 Jun 2020 02:56:52: 10000000 INFO @ Tue, 30 Jun 2020 02:56:57: 1000000 INFO @ Tue, 30 Jun 2020 02:56:59: 11000000 INFO @ Tue, 30 Jun 2020 02:57:00: 5000000 INFO @ Tue, 30 Jun 2020 02:57:04: 2000000 INFO @ Tue, 30 Jun 2020 02:57:05: 12000000 INFO @ Tue, 30 Jun 2020 02:57:07: 6000000 INFO @ Tue, 30 Jun 2020 02:57:10: 3000000 INFO @ Tue, 30 Jun 2020 02:57:11: 13000000 INFO @ Tue, 30 Jun 2020 02:57:15: 7000000 INFO @ Tue, 30 Jun 2020 02:57:17: 4000000 INFO @ Tue, 30 Jun 2020 02:57:18: 14000000 INFO @ Tue, 30 Jun 2020 02:57:23: 5000000 INFO @ Tue, 30 Jun 2020 02:57:23: 8000000 INFO @ Tue, 30 Jun 2020 02:57:24: 15000000 INFO @ Tue, 30 Jun 2020 02:57:29: 6000000 INFO @ Tue, 30 Jun 2020 02:57:31: 9000000 INFO @ Tue, 30 Jun 2020 02:57:31: 16000000 INFO @ Tue, 30 Jun 2020 02:57:36: 7000000 INFO @ Tue, 30 Jun 2020 02:57:37: 17000000 INFO @ Tue, 30 Jun 2020 02:57:38: 10000000 INFO @ Tue, 30 Jun 2020 02:57:42: 8000000 INFO @ Tue, 30 Jun 2020 02:57:44: 18000000 INFO @ Tue, 30 Jun 2020 02:57:46: 11000000 INFO @ Tue, 30 Jun 2020 02:57:48: 9000000 INFO @ Tue, 30 Jun 2020 02:57:49: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:57:49: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:57:49: #1 total tags in treatment: 18852865 INFO @ Tue, 30 Jun 2020 02:57:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:57:49: #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 02:57:50: #1 tags after filtering in treatment: 18852857 INFO @ Tue, 30 Jun 2020 02:57:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:57:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:57:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:57:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:57:51: #2 number of paired peaks: 106 WARNING @ Tue, 30 Jun 2020 02:57:51: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Tue, 30 Jun 2020 02:57:51: start model_add_line... INFO @ Tue, 30 Jun 2020 02:57:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:57:52: end of X-cor INFO @ Tue, 30 Jun 2020 02:57:52: #2 finished! INFO @ Tue, 30 Jun 2020 02:57:52: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 02:57:52: #2 alternative fragment length(s) may be 3,42 bps INFO @ Tue, 30 Jun 2020 02:57:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.05_model.r WARNING @ Tue, 30 Jun 2020 02:57:52: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:57:52: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Tue, 30 Jun 2020 02:57:52: #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 02:57:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:57:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:57:53: 12000000 INFO @ Tue, 30 Jun 2020 02:57:54: 10000000 INFO @ Tue, 30 Jun 2020 02:58:00: 11000000 INFO @ Tue, 30 Jun 2020 02:58:01: 13000000 INFO @ Tue, 30 Jun 2020 02:58:07: 12000000 INFO @ Tue, 30 Jun 2020 02:58:09: 14000000 INFO @ Tue, 30 Jun 2020 02:58:13: 13000000 INFO @ Tue, 30 Jun 2020 02:58:16: 15000000 INFO @ Tue, 30 Jun 2020 02:58:19: 14000000 INFO @ Tue, 30 Jun 2020 02:58:25: 16000000 INFO @ Tue, 30 Jun 2020 02:58:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:58:26: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:58:33: 17000000 INFO @ Tue, 30 Jun 2020 02:58:34: 16000000 INFO @ Tue, 30 Jun 2020 02:58:41: 18000000 INFO @ Tue, 30 Jun 2020 02:58:41: 17000000 INFO @ Tue, 30 Jun 2020 02:58:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:58:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:58:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.05_summits.bed INFO @ Tue, 30 Jun 2020 02:58:44: Done! pass1 - making usageList (419 chroms): 2 millis pass2 - checking and writing primary data (1553 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:58:48: 18000000 INFO @ Tue, 30 Jun 2020 02:58:48: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:58:48: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:58:48: #1 total tags in treatment: 18852865 INFO @ Tue, 30 Jun 2020 02:58:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:58:48: #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 02:58:48: #1 tags after filtering in treatment: 18852857 INFO @ Tue, 30 Jun 2020 02:58:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:58:48: #1 finished! INFO @ Tue, 30 Jun 2020 02:58:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:58:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:58:50: #2 number of paired peaks: 106 WARNING @ Tue, 30 Jun 2020 02:58:50: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Tue, 30 Jun 2020 02:58:50: start model_add_line... INFO @ Tue, 30 Jun 2020 02:58:50: start X-correlation... INFO @ Tue, 30 Jun 2020 02:58:50: end of X-cor INFO @ Tue, 30 Jun 2020 02:58:50: #2 finished! INFO @ Tue, 30 Jun 2020 02:58:50: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 02:58:50: #2 alternative fragment length(s) may be 3,42 bps INFO @ Tue, 30 Jun 2020 02:58:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.10_model.r WARNING @ Tue, 30 Jun 2020 02:58:50: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:58:50: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Tue, 30 Jun 2020 02:58:50: #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 02:58:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:58:54: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:58:54: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:58:54: #1 total tags in treatment: 18852865 INFO @ Tue, 30 Jun 2020 02:58:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:58:54: #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 02:58:55: #1 tags after filtering in treatment: 18852857 INFO @ Tue, 30 Jun 2020 02:58:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:58:55: #1 finished! INFO @ Tue, 30 Jun 2020 02:58:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:58:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:58:56: #2 number of paired peaks: 106 WARNING @ Tue, 30 Jun 2020 02:58:56: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Tue, 30 Jun 2020 02:58:56: start model_add_line... INFO @ Tue, 30 Jun 2020 02:58:56: start X-correlation... INFO @ Tue, 30 Jun 2020 02:58:56: end of X-cor INFO @ Tue, 30 Jun 2020 02:58:56: #2 finished! INFO @ Tue, 30 Jun 2020 02:58:56: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 02:58:56: #2 alternative fragment length(s) may be 3,42 bps INFO @ Tue, 30 Jun 2020 02:58:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.20_model.r WARNING @ Tue, 30 Jun 2020 02:58:56: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:58:56: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Tue, 30 Jun 2020 02:58:56: #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 02:58:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:58:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:59:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:59:30: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:59:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:59:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:59:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.10_summits.bed INFO @ Tue, 30 Jun 2020 02:59:41: Done! pass1 - making usageList (244 chroms): 1 millis pass2 - checking and writing primary data (522 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:59:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669053/SRX4669053.20_summits.bed INFO @ Tue, 30 Jun 2020 02:59:48: Done! pass1 - making usageList (85 chroms): 1 millis pass2 - checking and writing primary data (143 records, 4 fields): 6 millis CompletedMACS2peakCalling