Job ID = 6529747 SRX = SRX4669051 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: 00:04:39 22964650 reads; of these: 22964650 (100.00%) were unpaired; of these: 4507095 (19.63%) aligned 0 times 16368627 (71.28%) aligned exactly 1 time 2088928 (9.10%) aligned >1 times 80.37% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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 8 files... [bam_rmdupse_core] 3366299 / 18457555 = 0.1824 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 02:44:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.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 02:44:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:44:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:44:19: 1000000 INFO @ Tue, 30 Jun 2020 02:44:25: 2000000 INFO @ Tue, 30 Jun 2020 02:44:32: 3000000 INFO @ Tue, 30 Jun 2020 02:44:38: 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 02:44:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.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 02:44:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:44:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:44:45: 5000000 INFO @ Tue, 30 Jun 2020 02:44:49: 1000000 INFO @ Tue, 30 Jun 2020 02:44:51: 6000000 INFO @ Tue, 30 Jun 2020 02:44:56: 2000000 INFO @ Tue, 30 Jun 2020 02:44:57: 7000000 INFO @ Tue, 30 Jun 2020 02:45:02: 3000000 INFO @ Tue, 30 Jun 2020 02:45:03: 8000000 INFO @ Tue, 30 Jun 2020 02:45:08: 4000000 INFO @ Tue, 30 Jun 2020 02:45:09: 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 02:45:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.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 02:45:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:14: 5000000 INFO @ Tue, 30 Jun 2020 02:45:16: 10000000 INFO @ Tue, 30 Jun 2020 02:45:19: 1000000 INFO @ Tue, 30 Jun 2020 02:45:21: 6000000 INFO @ Tue, 30 Jun 2020 02:45:22: 11000000 INFO @ Tue, 30 Jun 2020 02:45:26: 2000000 INFO @ Tue, 30 Jun 2020 02:45:27: 7000000 INFO @ Tue, 30 Jun 2020 02:45:29: 12000000 INFO @ Tue, 30 Jun 2020 02:45:33: 3000000 INFO @ Tue, 30 Jun 2020 02:45:34: 8000000 INFO @ Tue, 30 Jun 2020 02:45:36: 13000000 INFO @ Tue, 30 Jun 2020 02:45:40: 9000000 INFO @ Tue, 30 Jun 2020 02:45:40: 4000000 INFO @ Tue, 30 Jun 2020 02:45:42: 14000000 INFO @ Tue, 30 Jun 2020 02:45:47: 10000000 INFO @ Tue, 30 Jun 2020 02:45:48: 5000000 INFO @ Tue, 30 Jun 2020 02:45:49: 15000000 INFO @ Tue, 30 Jun 2020 02:45:50: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:45:50: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:45:50: #1 total tags in treatment: 15091256 INFO @ Tue, 30 Jun 2020 02:45:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:45:50: #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 02:45:50: #1 tags after filtering in treatment: 15091212 INFO @ Tue, 30 Jun 2020 02:45:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:45:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:45:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:45:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:45:51: #2 number of paired peaks: 142 WARNING @ Tue, 30 Jun 2020 02:45:51: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Tue, 30 Jun 2020 02:45:51: start model_add_line... INFO @ Tue, 30 Jun 2020 02:45:52: start X-correlation... INFO @ Tue, 30 Jun 2020 02:45:52: end of X-cor INFO @ Tue, 30 Jun 2020 02:45:52: #2 finished! INFO @ Tue, 30 Jun 2020 02:45:52: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:45:52: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 30 Jun 2020 02:45:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.05_model.r WARNING @ Tue, 30 Jun 2020 02:45:52: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:45:52: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 30 Jun 2020 02:45:52: #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 02:45:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:45:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:45:53: 11000000 INFO @ Tue, 30 Jun 2020 02:45:55: 6000000 INFO @ Tue, 30 Jun 2020 02:45:58: 12000000 INFO @ Tue, 30 Jun 2020 02:46:02: 7000000 INFO @ Tue, 30 Jun 2020 02:46:05: 13000000 INFO @ Tue, 30 Jun 2020 02:46:09: 8000000 INFO @ Tue, 30 Jun 2020 02:46:10: 14000000 INFO @ Tue, 30 Jun 2020 02:46:16: 9000000 INFO @ Tue, 30 Jun 2020 02:46:16: 15000000 INFO @ Tue, 30 Jun 2020 02:46:17: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:46:17: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:46:17: #1 total tags in treatment: 15091256 INFO @ Tue, 30 Jun 2020 02:46:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:46:17: #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 02:46:18: #1 tags after filtering in treatment: 15091212 INFO @ Tue, 30 Jun 2020 02:46:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:46:18: #1 finished! INFO @ Tue, 30 Jun 2020 02:46:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:46:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:46:19: #2 number of paired peaks: 142 WARNING @ Tue, 30 Jun 2020 02:46:19: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Tue, 30 Jun 2020 02:46:19: start model_add_line... INFO @ Tue, 30 Jun 2020 02:46:19: start X-correlation... INFO @ Tue, 30 Jun 2020 02:46:19: end of X-cor INFO @ Tue, 30 Jun 2020 02:46:19: #2 finished! INFO @ Tue, 30 Jun 2020 02:46:19: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:46:19: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 30 Jun 2020 02:46:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.10_model.r WARNING @ Tue, 30 Jun 2020 02:46:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:46:19: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 30 Jun 2020 02:46:19: #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 02:46:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:46:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:46:20: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:46:22: 10000000 INFO @ Tue, 30 Jun 2020 02:46:29: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:46:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:46:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:46:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.05_summits.bed INFO @ Tue, 30 Jun 2020 02:46:35: Done! pass1 - making usageList (358 chroms): 1 millis pass2 - checking and writing primary data (2738 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:46:36: 12000000 INFO @ Tue, 30 Jun 2020 02:46:43: 13000000 INFO @ Tue, 30 Jun 2020 02:46:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:46:50: 14000000 INFO @ Tue, 30 Jun 2020 02:46:57: 15000000 INFO @ Tue, 30 Jun 2020 02:46:58: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:46:58: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:46:58: #1 total tags in treatment: 15091256 INFO @ Tue, 30 Jun 2020 02:46:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:46:58: #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 02:46:59: #1 tags after filtering in treatment: 15091212 INFO @ Tue, 30 Jun 2020 02:46:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:46:59: #1 finished! INFO @ Tue, 30 Jun 2020 02:46:59: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:46:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:47:00: #2 number of paired peaks: 142 WARNING @ Tue, 30 Jun 2020 02:47:00: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Tue, 30 Jun 2020 02:47:00: start model_add_line... INFO @ Tue, 30 Jun 2020 02:47:00: start X-correlation... INFO @ Tue, 30 Jun 2020 02:47:00: end of X-cor INFO @ Tue, 30 Jun 2020 02:47:00: #2 finished! INFO @ Tue, 30 Jun 2020 02:47:00: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:47:00: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 30 Jun 2020 02:47:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.20_model.r WARNING @ Tue, 30 Jun 2020 02:47:00: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:47:00: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 30 Jun 2020 02:47:00: #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 02:47:00: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:47:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:47:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:47:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:47:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.10_summits.bed INFO @ Tue, 30 Jun 2020 02:47:03: Done! pass1 - making usageList (195 chroms): 1 millis pass2 - checking and writing primary data (472 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:47:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:47:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:47:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:47:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669051/SRX4669051.20_summits.bed INFO @ Tue, 30 Jun 2020 02:47:45: Done! pass1 - making usageList (67 chroms): 1 millis pass2 - checking and writing primary data (113 records, 4 fields): 5 millis CompletedMACS2peakCalling