Job ID = 6529328 SRX = SRX1837298 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: 00:10:37 33930162 reads; of these: 33930162 (100.00%) were unpaired; of these: 4610070 (13.59%) aligned 0 times 11002854 (32.43%) aligned exactly 1 time 18317238 (53.99%) aligned >1 times 86.41% overall alignment rate Time searching: 00:10:37 Overall time: 00:10:37 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] 9435536 / 29320092 = 0.3218 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 02:05:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.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 02:05:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:05:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:05:30: 1000000 INFO @ Tue, 30 Jun 2020 02:05:35: 2000000 INFO @ Tue, 30 Jun 2020 02:05:40: 3000000 INFO @ Tue, 30 Jun 2020 02:05:45: 4000000 INFO @ Tue, 30 Jun 2020 02:05:50: 5000000 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 02:05:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.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 02:05:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:05:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:05:56: 6000000 INFO @ Tue, 30 Jun 2020 02:06:00: 1000000 INFO @ Tue, 30 Jun 2020 02:06:01: 7000000 INFO @ Tue, 30 Jun 2020 02:06:06: 2000000 INFO @ Tue, 30 Jun 2020 02:06:07: 8000000 INFO @ Tue, 30 Jun 2020 02:06:12: 3000000 INFO @ Tue, 30 Jun 2020 02:06:13: 9000000 INFO @ Tue, 30 Jun 2020 02:06:17: 4000000 INFO @ Tue, 30 Jun 2020 02:06:18: 10000000 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 02:06:23: 5000000 INFO @ Tue, 30 Jun 2020 02:06:24: 11000000 INFO @ Tue, 30 Jun 2020 02:06:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.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 02:06:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:06:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:06:29: 6000000 INFO @ Tue, 30 Jun 2020 02:06:30: 12000000 INFO @ Tue, 30 Jun 2020 02:06:30: 1000000 INFO @ Tue, 30 Jun 2020 02:06:35: 7000000 INFO @ Tue, 30 Jun 2020 02:06:35: 13000000 INFO @ Tue, 30 Jun 2020 02:06:36: 2000000 INFO @ Tue, 30 Jun 2020 02:06:41: 8000000 INFO @ Tue, 30 Jun 2020 02:06:41: 14000000 INFO @ Tue, 30 Jun 2020 02:06:42: 3000000 INFO @ Tue, 30 Jun 2020 02:06:47: 9000000 INFO @ Tue, 30 Jun 2020 02:06:47: 15000000 INFO @ Tue, 30 Jun 2020 02:06:47: 4000000 INFO @ Tue, 30 Jun 2020 02:06:52: 10000000 INFO @ Tue, 30 Jun 2020 02:06:53: 16000000 INFO @ Tue, 30 Jun 2020 02:06:53: 5000000 INFO @ Tue, 30 Jun 2020 02:06:58: 11000000 INFO @ Tue, 30 Jun 2020 02:06:59: 17000000 INFO @ Tue, 30 Jun 2020 02:06:59: 6000000 INFO @ Tue, 30 Jun 2020 02:07:04: 12000000 INFO @ Tue, 30 Jun 2020 02:07:05: 18000000 INFO @ Tue, 30 Jun 2020 02:07:05: 7000000 INFO @ Tue, 30 Jun 2020 02:07:10: 13000000 INFO @ Tue, 30 Jun 2020 02:07:10: 19000000 INFO @ Tue, 30 Jun 2020 02:07:11: 8000000 INFO @ Tue, 30 Jun 2020 02:07:16: 14000000 INFO @ Tue, 30 Jun 2020 02:07:16: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:07:16: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:07:16: #1 total tags in treatment: 19884556 INFO @ Tue, 30 Jun 2020 02:07:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:07:16: #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 02:07:16: #1 tags after filtering in treatment: 19884524 INFO @ Tue, 30 Jun 2020 02:07:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:07:16: #1 finished! INFO @ Tue, 30 Jun 2020 02:07:16: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:07:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:07:17: 9000000 INFO @ Tue, 30 Jun 2020 02:07:18: #2 number of paired peaks: 4317 INFO @ Tue, 30 Jun 2020 02:07:18: start model_add_line... INFO @ Tue, 30 Jun 2020 02:07:18: start X-correlation... INFO @ Tue, 30 Jun 2020 02:07:18: end of X-cor INFO @ Tue, 30 Jun 2020 02:07:18: #2 finished! INFO @ Tue, 30 Jun 2020 02:07:18: #2 predicted fragment length is 56 bps INFO @ Tue, 30 Jun 2020 02:07:18: #2 alternative fragment length(s) may be 2,56,593 bps INFO @ Tue, 30 Jun 2020 02:07:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.05_model.r WARNING @ Tue, 30 Jun 2020 02:07:18: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:07:18: #2 You may need to consider one of the other alternative d(s): 2,56,593 WARNING @ Tue, 30 Jun 2020 02:07:18: #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 02:07:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:07:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:07:22: 15000000 INFO @ Tue, 30 Jun 2020 02:07:23: 10000000 INFO @ Tue, 30 Jun 2020 02:07:27: 16000000 INFO @ Tue, 30 Jun 2020 02:07:29: 11000000 INFO @ Tue, 30 Jun 2020 02:07:33: 17000000 INFO @ Tue, 30 Jun 2020 02:07:34: 12000000 INFO @ Tue, 30 Jun 2020 02:07:39: 18000000 INFO @ Tue, 30 Jun 2020 02:07:40: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:07:45: 19000000 INFO @ Tue, 30 Jun 2020 02:07:46: 14000000 INFO @ Tue, 30 Jun 2020 02:07:50: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:07:50: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:07:50: #1 total tags in treatment: 19884556 INFO @ Tue, 30 Jun 2020 02:07:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:07:50: #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 02:07:50: #1 tags after filtering in treatment: 19884524 INFO @ Tue, 30 Jun 2020 02:07:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:07:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:07:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:07:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:07:52: #2 number of paired peaks: 4317 INFO @ Tue, 30 Jun 2020 02:07:52: start model_add_line... INFO @ Tue, 30 Jun 2020 02:07:52: 15000000 INFO @ Tue, 30 Jun 2020 02:07:52: start X-correlation... INFO @ Tue, 30 Jun 2020 02:07:52: end of X-cor INFO @ Tue, 30 Jun 2020 02:07:52: #2 finished! INFO @ Tue, 30 Jun 2020 02:07:52: #2 predicted fragment length is 56 bps INFO @ Tue, 30 Jun 2020 02:07:52: #2 alternative fragment length(s) may be 2,56,593 bps INFO @ Tue, 30 Jun 2020 02:07:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.10_model.r WARNING @ Tue, 30 Jun 2020 02:07:52: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:07:52: #2 You may need to consider one of the other alternative d(s): 2,56,593 WARNING @ Tue, 30 Jun 2020 02:07:52: #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 02:07:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:07:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:07:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:07:58: 16000000 INFO @ Tue, 30 Jun 2020 02:08:03: 17000000 INFO @ Tue, 30 Jun 2020 02:08:08: 18000000 INFO @ Tue, 30 Jun 2020 02:08:14: 19000000 INFO @ Tue, 30 Jun 2020 02:08:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:08:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:08:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.05_summits.bed INFO @ Tue, 30 Jun 2020 02:08:16: Done! pass1 - making usageList (1197 chroms): 3 millis pass2 - checking and writing primary data (7781 records, 4 fields): 38 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:08:18: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:08:18: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:08:18: #1 total tags in treatment: 19884556 INFO @ Tue, 30 Jun 2020 02:08:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:08:18: #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 02:08:19: #1 tags after filtering in treatment: 19884524 INFO @ Tue, 30 Jun 2020 02:08:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:08:19: #1 finished! INFO @ Tue, 30 Jun 2020 02:08:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:08:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:08:21: #2 number of paired peaks: 4317 INFO @ Tue, 30 Jun 2020 02:08:21: start model_add_line... INFO @ Tue, 30 Jun 2020 02:08:21: start X-correlation... INFO @ Tue, 30 Jun 2020 02:08:21: end of X-cor INFO @ Tue, 30 Jun 2020 02:08:21: #2 finished! INFO @ Tue, 30 Jun 2020 02:08:21: #2 predicted fragment length is 56 bps INFO @ Tue, 30 Jun 2020 02:08:21: #2 alternative fragment length(s) may be 2,56,593 bps INFO @ Tue, 30 Jun 2020 02:08:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.20_model.r WARNING @ Tue, 30 Jun 2020 02:08:21: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:08:21: #2 You may need to consider one of the other alternative d(s): 2,56,593 WARNING @ Tue, 30 Jun 2020 02:08:21: #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 02:08:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:08:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:08:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:08:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:08:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:08:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.10_summits.bed INFO @ Tue, 30 Jun 2020 02:08:46: Done! pass1 - making usageList (1005 chroms): 1 millis pass2 - checking and writing primary data (3831 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:08:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:09:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:09:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:09:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837298/SRX1837298.20_summits.bed INFO @ Tue, 30 Jun 2020 02:09:15: Done! pass1 - making usageList (693 chroms): 1 millis pass2 - checking and writing primary data (2315 records, 4 fields): 19 millis CompletedMACS2peakCalling