Job ID = 6529256 SRX = SRX1115698 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: 00:06:22 27426213 reads; of these: 27426213 (100.00%) were unpaired; of these: 1055439 (3.85%) aligned 0 times 20211437 (73.69%) aligned exactly 1 time 6159337 (22.46%) aligned >1 times 96.15% overall alignment rate Time searching: 00:06:22 Overall time: 00:06:22 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] 3223893 / 26370774 = 0.1223 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 01:42:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.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 01:42:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:42:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:42:42: 1000000 INFO @ Tue, 30 Jun 2020 01:42:51: 2000000 INFO @ Tue, 30 Jun 2020 01:42:58: 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 01:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.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 01:43:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:43:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:43:05: 4000000 INFO @ Tue, 30 Jun 2020 01:43:12: 1000000 INFO @ Tue, 30 Jun 2020 01:43:13: 5000000 INFO @ Tue, 30 Jun 2020 01:43:20: 2000000 INFO @ Tue, 30 Jun 2020 01:43:21: 6000000 INFO @ Tue, 30 Jun 2020 01:43:28: 3000000 INFO @ Tue, 30 Jun 2020 01:43:29: 7000000 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 01:43:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.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 01:43:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:43:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:43:36: 4000000 INFO @ Tue, 30 Jun 2020 01:43:38: 8000000 INFO @ Tue, 30 Jun 2020 01:43:42: 1000000 INFO @ Tue, 30 Jun 2020 01:43:44: 5000000 INFO @ Tue, 30 Jun 2020 01:43:46: 9000000 INFO @ Tue, 30 Jun 2020 01:43:50: 2000000 INFO @ Tue, 30 Jun 2020 01:43:52: 6000000 INFO @ Tue, 30 Jun 2020 01:43:54: 10000000 INFO @ Tue, 30 Jun 2020 01:43:58: 3000000 INFO @ Tue, 30 Jun 2020 01:44:00: 7000000 INFO @ Tue, 30 Jun 2020 01:44:02: 11000000 INFO @ Tue, 30 Jun 2020 01:44:06: 4000000 INFO @ Tue, 30 Jun 2020 01:44:08: 8000000 INFO @ Tue, 30 Jun 2020 01:44:11: 12000000 INFO @ Tue, 30 Jun 2020 01:44:14: 5000000 INFO @ Tue, 30 Jun 2020 01:44:16: 9000000 INFO @ Tue, 30 Jun 2020 01:44:19: 13000000 INFO @ Tue, 30 Jun 2020 01:44:22: 6000000 INFO @ Tue, 30 Jun 2020 01:44:25: 10000000 INFO @ Tue, 30 Jun 2020 01:44:27: 14000000 INFO @ Tue, 30 Jun 2020 01:44:30: 7000000 INFO @ Tue, 30 Jun 2020 01:44:33: 11000000 INFO @ Tue, 30 Jun 2020 01:44:36: 15000000 INFO @ Tue, 30 Jun 2020 01:44:38: 8000000 INFO @ Tue, 30 Jun 2020 01:44:42: 12000000 INFO @ Tue, 30 Jun 2020 01:44:44: 16000000 INFO @ Tue, 30 Jun 2020 01:44:47: 9000000 INFO @ Tue, 30 Jun 2020 01:44:50: 13000000 INFO @ Tue, 30 Jun 2020 01:44:53: 17000000 INFO @ Tue, 30 Jun 2020 01:44:55: 10000000 INFO @ Tue, 30 Jun 2020 01:44:59: 14000000 INFO @ Tue, 30 Jun 2020 01:45:01: 18000000 INFO @ Tue, 30 Jun 2020 01:45:04: 11000000 INFO @ Tue, 30 Jun 2020 01:45:07: 15000000 INFO @ Tue, 30 Jun 2020 01:45:10: 19000000 INFO @ Tue, 30 Jun 2020 01:45:12: 12000000 INFO @ Tue, 30 Jun 2020 01:45:16: 16000000 INFO @ Tue, 30 Jun 2020 01:45:19: 20000000 INFO @ Tue, 30 Jun 2020 01:45:21: 13000000 INFO @ Tue, 30 Jun 2020 01:45:24: 17000000 INFO @ Tue, 30 Jun 2020 01:45:28: 21000000 INFO @ Tue, 30 Jun 2020 01:45:29: 14000000 INFO @ Tue, 30 Jun 2020 01:45:32: 18000000 INFO @ Tue, 30 Jun 2020 01:45:37: 15000000 INFO @ Tue, 30 Jun 2020 01:45:37: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:45:41: 19000000 INFO @ Tue, 30 Jun 2020 01:45:45: 16000000 INFO @ Tue, 30 Jun 2020 01:45:46: 23000000 INFO @ Tue, 30 Jun 2020 01:45:48: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:45:48: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:45:48: #1 total tags in treatment: 23146881 INFO @ Tue, 30 Jun 2020 01:45:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:45:48: #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 01:45:49: #1 tags after filtering in treatment: 23146881 INFO @ Tue, 30 Jun 2020 01:45:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:45:49: #1 finished! INFO @ Tue, 30 Jun 2020 01:45:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:45:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:45:50: 20000000 INFO @ Tue, 30 Jun 2020 01:45:50: #2 number of paired peaks: 139 WARNING @ Tue, 30 Jun 2020 01:45:50: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Tue, 30 Jun 2020 01:45:50: start model_add_line... INFO @ Tue, 30 Jun 2020 01:45:50: start X-correlation... INFO @ Tue, 30 Jun 2020 01:45:50: end of X-cor INFO @ Tue, 30 Jun 2020 01:45:50: #2 finished! INFO @ Tue, 30 Jun 2020 01:45:50: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 01:45:50: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 30 Jun 2020 01:45:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.05_model.r WARNING @ Tue, 30 Jun 2020 01:45:50: #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 01:45:50: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 30 Jun 2020 01:45:50: #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 01:45:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:45:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:45:53: 17000000 INFO @ Tue, 30 Jun 2020 01:45:58: 21000000 INFO @ Tue, 30 Jun 2020 01:46:01: 18000000 INFO @ Tue, 30 Jun 2020 01:46:06: 22000000 INFO @ Tue, 30 Jun 2020 01:46:10: 19000000 INFO @ Tue, 30 Jun 2020 01:46:14: 23000000 INFO @ Tue, 30 Jun 2020 01:46:16: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:46:16: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:46:16: #1 total tags in treatment: 23146881 INFO @ Tue, 30 Jun 2020 01:46:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:46:16: #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 01:46:17: #1 tags after filtering in treatment: 23146881 INFO @ Tue, 30 Jun 2020 01:46:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:46:17: #1 finished! INFO @ Tue, 30 Jun 2020 01:46:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:46:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:46:18: 20000000 INFO @ Tue, 30 Jun 2020 01:46:18: #2 number of paired peaks: 139 WARNING @ Tue, 30 Jun 2020 01:46:18: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Tue, 30 Jun 2020 01:46:18: start model_add_line... INFO @ Tue, 30 Jun 2020 01:46:18: start X-correlation... INFO @ Tue, 30 Jun 2020 01:46:18: end of X-cor INFO @ Tue, 30 Jun 2020 01:46:18: #2 finished! INFO @ Tue, 30 Jun 2020 01:46:18: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 01:46:18: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 30 Jun 2020 01:46:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.10_model.r WARNING @ Tue, 30 Jun 2020 01:46:18: #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 01:46:18: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 30 Jun 2020 01:46:18: #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 01:46:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:46:26: 21000000 INFO @ Tue, 30 Jun 2020 01:46:28: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:46:33: 22000000 INFO @ Tue, 30 Jun 2020 01:46:41: 23000000 INFO @ Tue, 30 Jun 2020 01:46:43: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 01:46:43: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 01:46:43: #1 total tags in treatment: 23146881 INFO @ Tue, 30 Jun 2020 01:46:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:46:43: #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 01:46:43: #1 tags after filtering in treatment: 23146881 INFO @ Tue, 30 Jun 2020 01:46:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:46:43: #1 finished! INFO @ Tue, 30 Jun 2020 01:46:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:46:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:46:45: #2 number of paired peaks: 139 WARNING @ Tue, 30 Jun 2020 01:46:45: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Tue, 30 Jun 2020 01:46:45: start model_add_line... INFO @ Tue, 30 Jun 2020 01:46:45: start X-correlation... INFO @ Tue, 30 Jun 2020 01:46:45: end of X-cor INFO @ Tue, 30 Jun 2020 01:46:45: #2 finished! INFO @ Tue, 30 Jun 2020 01:46:45: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 01:46:45: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 30 Jun 2020 01:46:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.20_model.r WARNING @ Tue, 30 Jun 2020 01:46:45: #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 01:46:45: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 30 Jun 2020 01:46:45: #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 01:46:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:46:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:46:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:46:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:46:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.05_summits.bed INFO @ Tue, 30 Jun 2020 01:46:48: Done! pass1 - making usageList (569 chroms): 1 millis pass2 - checking and writing primary data (1916 records, 4 fields): 33 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:46:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:47:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:47:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:47:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.10_summits.bed INFO @ Tue, 30 Jun 2020 01:47:17: Done! pass1 - making usageList (344 chroms): 1 millis pass2 - checking and writing primary data (820 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:47:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:47:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:47:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:47:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1115698/SRX1115698.20_summits.bed INFO @ Tue, 30 Jun 2020 01:47:42: Done! pass1 - making usageList (135 chroms): 1 millis pass2 - checking and writing primary data (330 records, 4 fields): 9 millis CompletedMACS2peakCalling