Job ID = 6529935 SRX = SRX5379465 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: 00:07:56 33363864 reads; of these: 33363864 (100.00%) were unpaired; of these: 1289786 (3.87%) aligned 0 times 27503709 (82.44%) aligned exactly 1 time 4570369 (13.70%) aligned >1 times 96.13% overall alignment rate Time searching: 00:07:56 Overall time: 00:07:56 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 16 files... [bam_rmdupse_core] 4602115 / 32074078 = 0.1435 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 03:12:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.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 03:12:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:12:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:13:03: 1000000 INFO @ Tue, 30 Jun 2020 03:13:08: 2000000 INFO @ Tue, 30 Jun 2020 03:13:12: 3000000 INFO @ Tue, 30 Jun 2020 03:13:17: 4000000 INFO @ Tue, 30 Jun 2020 03:13:22: 5000000 INFO @ Tue, 30 Jun 2020 03:13:26: 6000000 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 03:13:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.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 03:13:28: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:13:28: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:13:31: 7000000 INFO @ Tue, 30 Jun 2020 03:13:33: 1000000 INFO @ Tue, 30 Jun 2020 03:13:36: 8000000 INFO @ Tue, 30 Jun 2020 03:13:38: 2000000 INFO @ Tue, 30 Jun 2020 03:13:41: 9000000 INFO @ Tue, 30 Jun 2020 03:13:43: 3000000 INFO @ Tue, 30 Jun 2020 03:13:46: 10000000 INFO @ Tue, 30 Jun 2020 03:13:48: 4000000 INFO @ Tue, 30 Jun 2020 03:13:51: 11000000 INFO @ Tue, 30 Jun 2020 03:13:53: 5000000 INFO @ Tue, 30 Jun 2020 03:13:56: 12000000 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 03:13:58: 6000000 INFO @ Tue, 30 Jun 2020 03:13:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.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 03:13:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:13:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:14:01: 13000000 INFO @ Tue, 30 Jun 2020 03:14:03: 7000000 INFO @ Tue, 30 Jun 2020 03:14:04: 1000000 INFO @ Tue, 30 Jun 2020 03:14:06: 14000000 INFO @ Tue, 30 Jun 2020 03:14:08: 8000000 INFO @ Tue, 30 Jun 2020 03:14:09: 2000000 INFO @ Tue, 30 Jun 2020 03:14:11: 15000000 INFO @ Tue, 30 Jun 2020 03:14:13: 9000000 INFO @ Tue, 30 Jun 2020 03:14:14: 3000000 INFO @ Tue, 30 Jun 2020 03:14:16: 16000000 INFO @ Tue, 30 Jun 2020 03:14:18: 10000000 INFO @ Tue, 30 Jun 2020 03:14:19: 4000000 INFO @ Tue, 30 Jun 2020 03:14:21: 17000000 INFO @ Tue, 30 Jun 2020 03:14:23: 11000000 INFO @ Tue, 30 Jun 2020 03:14:24: 5000000 INFO @ Tue, 30 Jun 2020 03:14:26: 18000000 INFO @ Tue, 30 Jun 2020 03:14:29: 12000000 INFO @ Tue, 30 Jun 2020 03:14:29: 6000000 INFO @ Tue, 30 Jun 2020 03:14:31: 19000000 INFO @ Tue, 30 Jun 2020 03:14:34: 13000000 INFO @ Tue, 30 Jun 2020 03:14:34: 7000000 INFO @ Tue, 30 Jun 2020 03:14:36: 20000000 INFO @ Tue, 30 Jun 2020 03:14:39: 14000000 INFO @ Tue, 30 Jun 2020 03:14:40: 8000000 INFO @ Tue, 30 Jun 2020 03:14:42: 21000000 INFO @ Tue, 30 Jun 2020 03:14:44: 15000000 INFO @ Tue, 30 Jun 2020 03:14:45: 9000000 INFO @ Tue, 30 Jun 2020 03:14:47: 22000000 INFO @ Tue, 30 Jun 2020 03:14:50: 16000000 INFO @ Tue, 30 Jun 2020 03:14:50: 10000000 INFO @ Tue, 30 Jun 2020 03:14:52: 23000000 INFO @ Tue, 30 Jun 2020 03:14:55: 17000000 INFO @ Tue, 30 Jun 2020 03:14:55: 11000000 INFO @ Tue, 30 Jun 2020 03:14:57: 24000000 INFO @ Tue, 30 Jun 2020 03:15:00: 18000000 INFO @ Tue, 30 Jun 2020 03:15:01: 12000000 INFO @ Tue, 30 Jun 2020 03:15:02: 25000000 INFO @ Tue, 30 Jun 2020 03:15:06: 19000000 INFO @ Tue, 30 Jun 2020 03:15:06: 13000000 INFO @ Tue, 30 Jun 2020 03:15:08: 26000000 INFO @ Tue, 30 Jun 2020 03:15:11: 20000000 INFO @ Tue, 30 Jun 2020 03:15:11: 14000000 INFO @ Tue, 30 Jun 2020 03:15:13: 27000000 INFO @ Tue, 30 Jun 2020 03:15:15: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:15:15: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:15:15: #1 total tags in treatment: 27471963 INFO @ Tue, 30 Jun 2020 03:15:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:15:15: #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 03:15:16: 21000000 INFO @ Tue, 30 Jun 2020 03:15:16: #1 tags after filtering in treatment: 27471883 INFO @ Tue, 30 Jun 2020 03:15:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:15:16: #1 finished! INFO @ Tue, 30 Jun 2020 03:15:16: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:15:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:15:17: 15000000 INFO @ Tue, 30 Jun 2020 03:15:18: #2 number of paired peaks: 137 WARNING @ Tue, 30 Jun 2020 03:15:18: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Tue, 30 Jun 2020 03:15:18: start model_add_line... INFO @ Tue, 30 Jun 2020 03:15:18: start X-correlation... INFO @ Tue, 30 Jun 2020 03:15:18: end of X-cor INFO @ Tue, 30 Jun 2020 03:15:18: #2 finished! INFO @ Tue, 30 Jun 2020 03:15:18: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 03:15:18: #2 alternative fragment length(s) may be 1,46 bps INFO @ Tue, 30 Jun 2020 03:15:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.05_model.r WARNING @ Tue, 30 Jun 2020 03:15:18: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:15:18: #2 You may need to consider one of the other alternative d(s): 1,46 WARNING @ Tue, 30 Jun 2020 03:15:18: #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 03:15:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:15:22: 22000000 INFO @ Tue, 30 Jun 2020 03:15:22: 16000000 INFO @ Tue, 30 Jun 2020 03:15:27: 23000000 INFO @ Tue, 30 Jun 2020 03:15:27: 17000000 INFO @ Tue, 30 Jun 2020 03:15:32: 24000000 INFO @ Tue, 30 Jun 2020 03:15:32: 18000000 INFO @ Tue, 30 Jun 2020 03:15:37: 25000000 INFO @ Tue, 30 Jun 2020 03:15:37: 19000000 INFO @ Tue, 30 Jun 2020 03:15:42: 26000000 INFO @ Tue, 30 Jun 2020 03:15:42: 20000000 INFO @ Tue, 30 Jun 2020 03:15:47: 27000000 INFO @ Tue, 30 Jun 2020 03:15:47: 21000000 INFO @ Tue, 30 Jun 2020 03:15:50: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:15:50: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:15:50: #1 total tags in treatment: 27471963 INFO @ Tue, 30 Jun 2020 03:15:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:15:50: #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 03:15:51: #1 tags after filtering in treatment: 27471883 INFO @ Tue, 30 Jun 2020 03:15:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:15:51: #1 finished! INFO @ Tue, 30 Jun 2020 03:15:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:15:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:15:53: 22000000 INFO @ Tue, 30 Jun 2020 03:15:53: #2 number of paired peaks: 137 WARNING @ Tue, 30 Jun 2020 03:15:53: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Tue, 30 Jun 2020 03:15:53: start model_add_line... INFO @ Tue, 30 Jun 2020 03:15:53: start X-correlation... INFO @ Tue, 30 Jun 2020 03:15:53: end of X-cor INFO @ Tue, 30 Jun 2020 03:15:53: #2 finished! INFO @ Tue, 30 Jun 2020 03:15:53: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 03:15:53: #2 alternative fragment length(s) may be 1,46 bps INFO @ Tue, 30 Jun 2020 03:15:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.10_model.r WARNING @ Tue, 30 Jun 2020 03:15:53: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:15:53: #2 You may need to consider one of the other alternative d(s): 1,46 WARNING @ Tue, 30 Jun 2020 03:15:53: #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 03:15:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:15:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:15:58: 23000000 INFO @ Tue, 30 Jun 2020 03:16:03: 24000000 INFO @ Tue, 30 Jun 2020 03:16:08: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:16:08: 25000000 INFO @ Tue, 30 Jun 2020 03:16:13: 26000000 INFO @ Tue, 30 Jun 2020 03:16:18: 27000000 INFO @ Tue, 30 Jun 2020 03:16:21: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:16:21: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:16:21: #1 total tags in treatment: 27471963 INFO @ Tue, 30 Jun 2020 03:16:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:16:21: #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 03:16:22: #1 tags after filtering in treatment: 27471883 INFO @ Tue, 30 Jun 2020 03:16:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:16:22: #1 finished! INFO @ Tue, 30 Jun 2020 03:16:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:16:24: #2 number of paired peaks: 137 WARNING @ Tue, 30 Jun 2020 03:16:24: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Tue, 30 Jun 2020 03:16:24: start model_add_line... BedGraph に変換しました。 INFO @ Tue, 30 Jun 2020 03:16:24: start X-correlation... BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:16:24: end of X-cor INFO @ Tue, 30 Jun 2020 03:16:24: #2 finished! INFO @ Tue, 30 Jun 2020 03:16:24: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 03:16:24: #2 alternative fragment length(s) may be 1,46 bps INFO @ Tue, 30 Jun 2020 03:16:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.20_model.r WARNING @ Tue, 30 Jun 2020 03:16:24: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:16:24: #2 You may need to consider one of the other alternative d(s): 1,46 WARNING @ Tue, 30 Jun 2020 03:16:24: #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 03:16:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:16:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:16:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:16:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:16:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.05_summits.bed INFO @ Tue, 30 Jun 2020 03:16:33: Done! pass1 - making usageList (293 chroms): 1 millis pass2 - checking and writing primary data (852 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:16:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:17:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:17:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:17:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.10_summits.bed INFO @ Tue, 30 Jun 2020 03:17:11: Done! pass1 - making usageList (150 chroms): 1 millis pass2 - checking and writing primary data (430 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:17:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:17:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:17:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:17:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5379465/SRX5379465.20_summits.bed INFO @ Tue, 30 Jun 2020 03:17:36: Done! pass1 - making usageList (88 chroms): 1 millis pass2 - checking and writing primary data (254 records, 4 fields): 3 millis CompletedMACS2peakCalling