Job ID = 6530109 SRX = SRX969931 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: 00:09:18 29782622 reads; of these: 29782622 (100.00%) were unpaired; of these: 1726843 (5.80%) aligned 0 times 19876170 (66.74%) aligned exactly 1 time 8179609 (27.46%) aligned >1 times 94.20% overall alignment rate Time searching: 00:09:18 Overall time: 00:09:18 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] 4911406 / 28055779 = 0.1751 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 03:35:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.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 03:35:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:35:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:35:26: 1000000 INFO @ Tue, 30 Jun 2020 03:35:31: 2000000 INFO @ Tue, 30 Jun 2020 03:35:36: 3000000 INFO @ Tue, 30 Jun 2020 03:35:42: 4000000 INFO @ Tue, 30 Jun 2020 03:35:47: 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 03:35:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.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 03:35:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:35:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:35:52: 6000000 INFO @ Tue, 30 Jun 2020 03:35:57: 1000000 INFO @ Tue, 30 Jun 2020 03:35:58: 7000000 INFO @ Tue, 30 Jun 2020 03:36:04: 2000000 INFO @ Tue, 30 Jun 2020 03:36:04: 8000000 INFO @ Tue, 30 Jun 2020 03:36:10: 9000000 INFO @ Tue, 30 Jun 2020 03:36:11: 3000000 INFO @ Tue, 30 Jun 2020 03:36:16: 10000000 INFO @ Tue, 30 Jun 2020 03:36:17: 4000000 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 03:36:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.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 03:36:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:36:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:36:22: 11000000 INFO @ Tue, 30 Jun 2020 03:36:24: 5000000 INFO @ Tue, 30 Jun 2020 03:36:28: 1000000 INFO @ Tue, 30 Jun 2020 03:36:28: 12000000 INFO @ Tue, 30 Jun 2020 03:36:31: 6000000 INFO @ Tue, 30 Jun 2020 03:36:34: 13000000 INFO @ Tue, 30 Jun 2020 03:36:34: 2000000 INFO @ Tue, 30 Jun 2020 03:36:37: 7000000 INFO @ Tue, 30 Jun 2020 03:36:40: 14000000 INFO @ Tue, 30 Jun 2020 03:36:41: 3000000 INFO @ Tue, 30 Jun 2020 03:36:44: 8000000 INFO @ Tue, 30 Jun 2020 03:36:46: 15000000 INFO @ Tue, 30 Jun 2020 03:36:47: 4000000 INFO @ Tue, 30 Jun 2020 03:36:50: 9000000 INFO @ Tue, 30 Jun 2020 03:36:52: 16000000 INFO @ Tue, 30 Jun 2020 03:36:54: 5000000 INFO @ Tue, 30 Jun 2020 03:36:57: 10000000 INFO @ Tue, 30 Jun 2020 03:36:58: 17000000 INFO @ Tue, 30 Jun 2020 03:37:01: 6000000 INFO @ Tue, 30 Jun 2020 03:37:04: 18000000 INFO @ Tue, 30 Jun 2020 03:37:04: 11000000 INFO @ Tue, 30 Jun 2020 03:37:07: 7000000 INFO @ Tue, 30 Jun 2020 03:37:10: 19000000 INFO @ Tue, 30 Jun 2020 03:37:10: 12000000 INFO @ Tue, 30 Jun 2020 03:37:14: 8000000 INFO @ Tue, 30 Jun 2020 03:37:16: 20000000 INFO @ Tue, 30 Jun 2020 03:37:17: 13000000 INFO @ Tue, 30 Jun 2020 03:37:21: 9000000 INFO @ Tue, 30 Jun 2020 03:37:22: 21000000 INFO @ Tue, 30 Jun 2020 03:37:23: 14000000 INFO @ Tue, 30 Jun 2020 03:37:27: 10000000 INFO @ Tue, 30 Jun 2020 03:37:28: 22000000 INFO @ Tue, 30 Jun 2020 03:37:30: 15000000 INFO @ Tue, 30 Jun 2020 03:37:34: 11000000 INFO @ Tue, 30 Jun 2020 03:37:34: 23000000 INFO @ Tue, 30 Jun 2020 03:37:35: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:37:35: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:37:35: #1 total tags in treatment: 23144373 INFO @ Tue, 30 Jun 2020 03:37:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:37:35: #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 03:37:36: #1 tags after filtering in treatment: 23144372 INFO @ Tue, 30 Jun 2020 03:37:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:37:36: #1 finished! INFO @ Tue, 30 Jun 2020 03:37:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:37:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:37:37: 16000000 INFO @ Tue, 30 Jun 2020 03:37:37: #2 number of paired peaks: 434 WARNING @ Tue, 30 Jun 2020 03:37:37: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Tue, 30 Jun 2020 03:37:37: start model_add_line... INFO @ Tue, 30 Jun 2020 03:37:37: start X-correlation... INFO @ Tue, 30 Jun 2020 03:37:37: end of X-cor INFO @ Tue, 30 Jun 2020 03:37:37: #2 finished! INFO @ Tue, 30 Jun 2020 03:37:37: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 03:37:37: #2 alternative fragment length(s) may be 2,14,556 bps INFO @ Tue, 30 Jun 2020 03:37:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.05_model.r WARNING @ Tue, 30 Jun 2020 03:37:37: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:37:37: #2 You may need to consider one of the other alternative d(s): 2,14,556 WARNING @ Tue, 30 Jun 2020 03:37:37: #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 03:37:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:37:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:37:40: 12000000 INFO @ Tue, 30 Jun 2020 03:37:43: 17000000 INFO @ Tue, 30 Jun 2020 03:37:47: 13000000 INFO @ Tue, 30 Jun 2020 03:37:50: 18000000 INFO @ Tue, 30 Jun 2020 03:37:54: 14000000 INFO @ Tue, 30 Jun 2020 03:37:57: 19000000 INFO @ Tue, 30 Jun 2020 03:38:00: 15000000 INFO @ Tue, 30 Jun 2020 03:38:03: 20000000 INFO @ Tue, 30 Jun 2020 03:38:07: 16000000 INFO @ Tue, 30 Jun 2020 03:38:10: 21000000 INFO @ Tue, 30 Jun 2020 03:38:13: 17000000 INFO @ Tue, 30 Jun 2020 03:38:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:38:16: 22000000 INFO @ Tue, 30 Jun 2020 03:38:20: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:38:23: 23000000 INFO @ Tue, 30 Jun 2020 03:38:24: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:38:24: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:38:24: #1 total tags in treatment: 23144373 INFO @ Tue, 30 Jun 2020 03:38:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:38:24: #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 03:38:25: #1 tags after filtering in treatment: 23144372 INFO @ Tue, 30 Jun 2020 03:38:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:38:25: #1 finished! INFO @ Tue, 30 Jun 2020 03:38:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:38:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:38:26: #2 number of paired peaks: 434 WARNING @ Tue, 30 Jun 2020 03:38:26: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Tue, 30 Jun 2020 03:38:26: start model_add_line... INFO @ Tue, 30 Jun 2020 03:38:27: start X-correlation... INFO @ Tue, 30 Jun 2020 03:38:27: end of X-cor INFO @ Tue, 30 Jun 2020 03:38:27: #2 finished! INFO @ Tue, 30 Jun 2020 03:38:27: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 03:38:27: #2 alternative fragment length(s) may be 2,14,556 bps INFO @ Tue, 30 Jun 2020 03:38:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.10_model.r WARNING @ Tue, 30 Jun 2020 03:38:27: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:38:27: #2 You may need to consider one of the other alternative d(s): 2,14,556 WARNING @ Tue, 30 Jun 2020 03:38:27: #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 03:38:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:38:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:38:27: 19000000 INFO @ Tue, 30 Jun 2020 03:38:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:38:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:38:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.05_summits.bed INFO @ Tue, 30 Jun 2020 03:38:33: Done! INFO @ Tue, 30 Jun 2020 03:38:33: 20000000 pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:38:39: 21000000 INFO @ Tue, 30 Jun 2020 03:38:45: 22000000 INFO @ Tue, 30 Jun 2020 03:38:52: 23000000 INFO @ Tue, 30 Jun 2020 03:38:53: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:38:53: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:38:53: #1 total tags in treatment: 23144373 INFO @ Tue, 30 Jun 2020 03:38:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:38:53: #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 03:38:53: #1 tags after filtering in treatment: 23144372 INFO @ Tue, 30 Jun 2020 03:38:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:38:53: #1 finished! INFO @ Tue, 30 Jun 2020 03:38:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:38:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:38:55: #2 number of paired peaks: 434 WARNING @ Tue, 30 Jun 2020 03:38:55: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Tue, 30 Jun 2020 03:38:55: start model_add_line... INFO @ Tue, 30 Jun 2020 03:38:55: start X-correlation... INFO @ Tue, 30 Jun 2020 03:38:55: end of X-cor INFO @ Tue, 30 Jun 2020 03:38:55: #2 finished! INFO @ Tue, 30 Jun 2020 03:38:55: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 03:38:55: #2 alternative fragment length(s) may be 2,14,556 bps INFO @ Tue, 30 Jun 2020 03:38:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.20_model.r WARNING @ Tue, 30 Jun 2020 03:38:55: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:38:55: #2 You may need to consider one of the other alternative d(s): 2,14,556 WARNING @ Tue, 30 Jun 2020 03:38:55: #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 03:38:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:38:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:39:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:39:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:39:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:39:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.10_summits.bed INFO @ Tue, 30 Jun 2020 03:39:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:39:32: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:39:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:39:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:39:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969931/SRX969931.20_summits.bed INFO @ Tue, 30 Jun 2020 03:39:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling