Job ID = 6529655 SRX = SRX385809 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: 00:08:10 27474174 reads; of these: 27474174 (100.00%) were unpaired; of these: 634324 (2.31%) aligned 0 times 19505354 (71.00%) aligned exactly 1 time 7334496 (26.70%) aligned >1 times 97.69% overall alignment rate Time searching: 00:08:10 Overall time: 00:08:10 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] 3676224 / 26839850 = 0.1370 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 02:37:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.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 02:37:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:37:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:37:07: 1000000 INFO @ Tue, 30 Jun 2020 02:37:13: 2000000 INFO @ Tue, 30 Jun 2020 02:37:18: 3000000 INFO @ Tue, 30 Jun 2020 02:37:24: 4000000 INFO @ Tue, 30 Jun 2020 02:37:29: 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 02:37:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.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 02:37:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:37:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:37:35: 6000000 INFO @ Tue, 30 Jun 2020 02:37:38: 1000000 INFO @ Tue, 30 Jun 2020 02:37:41: 7000000 INFO @ Tue, 30 Jun 2020 02:37:44: 2000000 INFO @ Tue, 30 Jun 2020 02:37:47: 8000000 INFO @ Tue, 30 Jun 2020 02:37:50: 3000000 INFO @ Tue, 30 Jun 2020 02:37:53: 9000000 INFO @ Tue, 30 Jun 2020 02:37:56: 4000000 INFO @ Tue, 30 Jun 2020 02:37:58: 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 02:38:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.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 02:38:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:38:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:38:02: 5000000 INFO @ Tue, 30 Jun 2020 02:38:04: 11000000 INFO @ Tue, 30 Jun 2020 02:38:08: 1000000 INFO @ Tue, 30 Jun 2020 02:38:08: 6000000 INFO @ Tue, 30 Jun 2020 02:38:10: 12000000 INFO @ Tue, 30 Jun 2020 02:38:14: 2000000 INFO @ Tue, 30 Jun 2020 02:38:15: 7000000 INFO @ Tue, 30 Jun 2020 02:38:16: 13000000 INFO @ Tue, 30 Jun 2020 02:38:20: 3000000 INFO @ Tue, 30 Jun 2020 02:38:21: 8000000 INFO @ Tue, 30 Jun 2020 02:38:22: 14000000 INFO @ Tue, 30 Jun 2020 02:38:26: 4000000 INFO @ Tue, 30 Jun 2020 02:38:27: 9000000 INFO @ Tue, 30 Jun 2020 02:38:28: 15000000 INFO @ Tue, 30 Jun 2020 02:38:32: 5000000 INFO @ Tue, 30 Jun 2020 02:38:33: 10000000 INFO @ Tue, 30 Jun 2020 02:38:34: 16000000 INFO @ Tue, 30 Jun 2020 02:38:39: 6000000 INFO @ Tue, 30 Jun 2020 02:38:40: 11000000 INFO @ Tue, 30 Jun 2020 02:38:40: 17000000 INFO @ Tue, 30 Jun 2020 02:38:45: 7000000 INFO @ Tue, 30 Jun 2020 02:38:46: 12000000 INFO @ Tue, 30 Jun 2020 02:38:47: 18000000 INFO @ Tue, 30 Jun 2020 02:38:51: 8000000 INFO @ Tue, 30 Jun 2020 02:38:52: 13000000 INFO @ Tue, 30 Jun 2020 02:38:53: 19000000 INFO @ Tue, 30 Jun 2020 02:38:57: 9000000 INFO @ Tue, 30 Jun 2020 02:38:58: 14000000 INFO @ Tue, 30 Jun 2020 02:38:59: 20000000 INFO @ Tue, 30 Jun 2020 02:39:03: 10000000 INFO @ Tue, 30 Jun 2020 02:39:04: 15000000 INFO @ Tue, 30 Jun 2020 02:39:05: 21000000 INFO @ Tue, 30 Jun 2020 02:39:09: 11000000 INFO @ Tue, 30 Jun 2020 02:39:10: 16000000 INFO @ Tue, 30 Jun 2020 02:39:11: 22000000 INFO @ Tue, 30 Jun 2020 02:39:15: 12000000 INFO @ Tue, 30 Jun 2020 02:39:16: 17000000 INFO @ Tue, 30 Jun 2020 02:39:17: 23000000 INFO @ Tue, 30 Jun 2020 02:39:19: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:39:19: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:39:19: #1 total tags in treatment: 23163626 INFO @ Tue, 30 Jun 2020 02:39:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:39:19: #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 02:39:19: #1 tags after filtering in treatment: 23163567 INFO @ Tue, 30 Jun 2020 02:39:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:39:19: #1 finished! INFO @ Tue, 30 Jun 2020 02:39:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:39:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:39:21: #2 number of paired peaks: 433 WARNING @ Tue, 30 Jun 2020 02:39:21: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Tue, 30 Jun 2020 02:39:21: start model_add_line... INFO @ Tue, 30 Jun 2020 02:39:21: 13000000 INFO @ Tue, 30 Jun 2020 02:39:21: start X-correlation... INFO @ Tue, 30 Jun 2020 02:39:21: end of X-cor INFO @ Tue, 30 Jun 2020 02:39:21: #2 finished! INFO @ Tue, 30 Jun 2020 02:39:21: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:39:21: #2 alternative fragment length(s) may be 1,47,538,568,589 bps INFO @ Tue, 30 Jun 2020 02:39:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.05_model.r WARNING @ Tue, 30 Jun 2020 02:39:21: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:39:21: #2 You may need to consider one of the other alternative d(s): 1,47,538,568,589 WARNING @ Tue, 30 Jun 2020 02:39:21: #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 02:39:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:39:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:39:22: 18000000 INFO @ Tue, 30 Jun 2020 02:39:27: 14000000 INFO @ Tue, 30 Jun 2020 02:39:28: 19000000 INFO @ Tue, 30 Jun 2020 02:39:33: 15000000 INFO @ Tue, 30 Jun 2020 02:39:35: 20000000 INFO @ Tue, 30 Jun 2020 02:39:38: 16000000 INFO @ Tue, 30 Jun 2020 02:39:41: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:39:44: 17000000 INFO @ Tue, 30 Jun 2020 02:39:47: 22000000 INFO @ Tue, 30 Jun 2020 02:39:50: 18000000 INFO @ Tue, 30 Jun 2020 02:39:53: 23000000 INFO @ Tue, 30 Jun 2020 02:39:54: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:39:54: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:39:54: #1 total tags in treatment: 23163626 INFO @ Tue, 30 Jun 2020 02:39:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:39:54: #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 02:39:55: #1 tags after filtering in treatment: 23163567 INFO @ Tue, 30 Jun 2020 02:39:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:39:55: #1 finished! INFO @ Tue, 30 Jun 2020 02:39:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:39:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:39:56: 19000000 INFO @ Tue, 30 Jun 2020 02:39:57: #2 number of paired peaks: 433 WARNING @ Tue, 30 Jun 2020 02:39:57: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Tue, 30 Jun 2020 02:39:57: start model_add_line... INFO @ Tue, 30 Jun 2020 02:39:57: start X-correlation... INFO @ Tue, 30 Jun 2020 02:39:57: end of X-cor INFO @ Tue, 30 Jun 2020 02:39:57: #2 finished! INFO @ Tue, 30 Jun 2020 02:39:57: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:39:57: #2 alternative fragment length(s) may be 1,47,538,568,589 bps INFO @ Tue, 30 Jun 2020 02:39:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.10_model.r WARNING @ Tue, 30 Jun 2020 02:39:57: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:39:57: #2 You may need to consider one of the other alternative d(s): 1,47,538,568,589 WARNING @ Tue, 30 Jun 2020 02:39:57: #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 02:39:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:39:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:40:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:40:02: 20000000 INFO @ Tue, 30 Jun 2020 02:40:08: 21000000 INFO @ Tue, 30 Jun 2020 02:40:14: 22000000 INFO @ Tue, 30 Jun 2020 02:40:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:40:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:40:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.05_summits.bed INFO @ Tue, 30 Jun 2020 02:40:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:40:20: 23000000 INFO @ Tue, 30 Jun 2020 02:40:21: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:40:21: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:40:21: #1 total tags in treatment: 23163626 INFO @ Tue, 30 Jun 2020 02:40:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:40:21: #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 02:40:22: #1 tags after filtering in treatment: 23163567 INFO @ Tue, 30 Jun 2020 02:40:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:40:22: #1 finished! INFO @ Tue, 30 Jun 2020 02:40:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:40:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:40:23: #2 number of paired peaks: 433 WARNING @ Tue, 30 Jun 2020 02:40:23: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Tue, 30 Jun 2020 02:40:23: start model_add_line... INFO @ Tue, 30 Jun 2020 02:40:23: start X-correlation... INFO @ Tue, 30 Jun 2020 02:40:23: end of X-cor INFO @ Tue, 30 Jun 2020 02:40:23: #2 finished! INFO @ Tue, 30 Jun 2020 02:40:23: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:40:23: #2 alternative fragment length(s) may be 1,47,538,568,589 bps INFO @ Tue, 30 Jun 2020 02:40:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.20_model.r WARNING @ Tue, 30 Jun 2020 02:40:23: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:40:23: #2 You may need to consider one of the other alternative d(s): 1,47,538,568,589 WARNING @ Tue, 30 Jun 2020 02:40:23: #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 02:40:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:40:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:40:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:40:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:40:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:40:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.10_summits.bed INFO @ Tue, 30 Jun 2020 02:40:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:41:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:41:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:41:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:41:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX385809/SRX385809.20_summits.bed INFO @ Tue, 30 Jun 2020 02:41:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling