Job ID = 6529325 SRX = SRX182777 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: 00:09:40 29700681 reads; of these: 29700681 (100.00%) were unpaired; of these: 2247892 (7.57%) aligned 0 times 17545695 (59.08%) aligned exactly 1 time 9907094 (33.36%) aligned >1 times 92.43% overall alignment rate Time searching: 00:09:40 Overall time: 00:09:40 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 8 files... [bam_rmdupse_core] 7316337 / 27452789 = 0.2665 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 01:57:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.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 01:57:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:58:04: 1000000 INFO @ Tue, 30 Jun 2020 01:58:12: 2000000 INFO @ Tue, 30 Jun 2020 01:58:20: 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 01:58:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.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 01:58:27: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:58:27: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:58:28: 4000000 INFO @ Tue, 30 Jun 2020 01:58:35: 1000000 INFO @ Tue, 30 Jun 2020 01:58:36: 5000000 INFO @ Tue, 30 Jun 2020 01:58:43: 2000000 INFO @ Tue, 30 Jun 2020 01:58:44: 6000000 INFO @ Tue, 30 Jun 2020 01:58:51: 3000000 INFO @ Tue, 30 Jun 2020 01:58:52: 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 01:58:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.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 01:58:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:58:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:58:59: 4000000 INFO @ Tue, 30 Jun 2020 01:58:59: 8000000 INFO @ Tue, 30 Jun 2020 01:59:04: 1000000 INFO @ Tue, 30 Jun 2020 01:59:07: 5000000 INFO @ Tue, 30 Jun 2020 01:59:07: 9000000 INFO @ Tue, 30 Jun 2020 01:59:11: 2000000 INFO @ Tue, 30 Jun 2020 01:59:15: 6000000 INFO @ Tue, 30 Jun 2020 01:59:15: 10000000 INFO @ Tue, 30 Jun 2020 01:59:19: 3000000 INFO @ Tue, 30 Jun 2020 01:59:22: 7000000 INFO @ Tue, 30 Jun 2020 01:59:23: 11000000 INFO @ Tue, 30 Jun 2020 01:59:26: 4000000 INFO @ Tue, 30 Jun 2020 01:59:30: 8000000 INFO @ Tue, 30 Jun 2020 01:59:31: 12000000 INFO @ Tue, 30 Jun 2020 01:59:34: 5000000 INFO @ Tue, 30 Jun 2020 01:59:38: 9000000 INFO @ Tue, 30 Jun 2020 01:59:39: 13000000 INFO @ Tue, 30 Jun 2020 01:59:41: 6000000 INFO @ Tue, 30 Jun 2020 01:59:46: 10000000 INFO @ Tue, 30 Jun 2020 01:59:46: 14000000 INFO @ Tue, 30 Jun 2020 01:59:49: 7000000 INFO @ Tue, 30 Jun 2020 01:59:53: 11000000 INFO @ Tue, 30 Jun 2020 01:59:54: 15000000 INFO @ Tue, 30 Jun 2020 01:59:56: 8000000 INFO @ Tue, 30 Jun 2020 02:00:01: 12000000 INFO @ Tue, 30 Jun 2020 02:00:02: 16000000 INFO @ Tue, 30 Jun 2020 02:00:03: 9000000 INFO @ Tue, 30 Jun 2020 02:00:08: 13000000 INFO @ Tue, 30 Jun 2020 02:00:10: 17000000 INFO @ Tue, 30 Jun 2020 02:00:10: 10000000 INFO @ Tue, 30 Jun 2020 02:00:16: 14000000 INFO @ Tue, 30 Jun 2020 02:00:17: 18000000 INFO @ Tue, 30 Jun 2020 02:00:18: 11000000 INFO @ Tue, 30 Jun 2020 02:00:23: 15000000 INFO @ Tue, 30 Jun 2020 02:00:25: 12000000 INFO @ Tue, 30 Jun 2020 02:00:25: 19000000 INFO @ Tue, 30 Jun 2020 02:00:31: 16000000 INFO @ Tue, 30 Jun 2020 02:00:32: 13000000 INFO @ Tue, 30 Jun 2020 02:00:33: 20000000 INFO @ Tue, 30 Jun 2020 02:00:34: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 02:00:34: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 02:00:34: #1 total tags in treatment: 20136452 INFO @ Tue, 30 Jun 2020 02:00:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:00:34: #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 02:00:35: #1 tags after filtering in treatment: 20136452 INFO @ Tue, 30 Jun 2020 02:00:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:00:35: #1 finished! INFO @ Tue, 30 Jun 2020 02:00:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:00:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:00:36: #2 number of paired peaks: 869 WARNING @ Tue, 30 Jun 2020 02:00:36: Fewer paired peaks (869) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 869 pairs to build model! INFO @ Tue, 30 Jun 2020 02:00:36: start model_add_line... INFO @ Tue, 30 Jun 2020 02:00:36: start X-correlation... INFO @ Tue, 30 Jun 2020 02:00:36: end of X-cor INFO @ Tue, 30 Jun 2020 02:00:36: #2 finished! INFO @ Tue, 30 Jun 2020 02:00:36: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:00:36: #2 alternative fragment length(s) may be 2,16,20 bps INFO @ Tue, 30 Jun 2020 02:00:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.05_model.r WARNING @ Tue, 30 Jun 2020 02:00:36: #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 02:00:36: #2 You may need to consider one of the other alternative d(s): 2,16,20 WARNING @ Tue, 30 Jun 2020 02:00:36: #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 02:00:36: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:00:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:00:39: 17000000 INFO @ Tue, 30 Jun 2020 02:00:39: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:00:46: 18000000 INFO @ Tue, 30 Jun 2020 02:00:46: 15000000 INFO @ Tue, 30 Jun 2020 02:00:53: 19000000 INFO @ Tue, 30 Jun 2020 02:00:54: 16000000 INFO @ Tue, 30 Jun 2020 02:01:01: 20000000 INFO @ Tue, 30 Jun 2020 02:01:01: 17000000 INFO @ Tue, 30 Jun 2020 02:01:02: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 02:01:02: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 02:01:02: #1 total tags in treatment: 20136452 INFO @ Tue, 30 Jun 2020 02:01:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:01:02: #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 02:01:03: #1 tags after filtering in treatment: 20136452 INFO @ Tue, 30 Jun 2020 02:01:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:01:03: #1 finished! INFO @ Tue, 30 Jun 2020 02:01:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:01:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:01:04: #2 number of paired peaks: 869 WARNING @ Tue, 30 Jun 2020 02:01:04: Fewer paired peaks (869) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 869 pairs to build model! INFO @ Tue, 30 Jun 2020 02:01:04: start model_add_line... INFO @ Tue, 30 Jun 2020 02:01:04: start X-correlation... INFO @ Tue, 30 Jun 2020 02:01:04: end of X-cor INFO @ Tue, 30 Jun 2020 02:01:04: #2 finished! INFO @ Tue, 30 Jun 2020 02:01:04: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:01:04: #2 alternative fragment length(s) may be 2,16,20 bps INFO @ Tue, 30 Jun 2020 02:01:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.10_model.r WARNING @ Tue, 30 Jun 2020 02:01:04: #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 02:01:04: #2 You may need to consider one of the other alternative d(s): 2,16,20 WARNING @ Tue, 30 Jun 2020 02:01:04: #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 02:01:04: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:01:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:01:08: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:01:08: 18000000 INFO @ Tue, 30 Jun 2020 02:01:15: 19000000 INFO @ Tue, 30 Jun 2020 02:01:23: 20000000 INFO @ Tue, 30 Jun 2020 02:01:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:01:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:01:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.05_summits.bed INFO @ Tue, 30 Jun 2020 02:01:24: Done! INFO @ Tue, 30 Jun 2020 02:01:24: #1 tag size is determined as 40 bps INFO @ Tue, 30 Jun 2020 02:01:24: #1 tag size = 40 INFO @ Tue, 30 Jun 2020 02:01:24: #1 total tags in treatment: 20136452 INFO @ Tue, 30 Jun 2020 02:01:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:01:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:01:25: #1 tags after filtering in treatment: 20136452 INFO @ Tue, 30 Jun 2020 02:01:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:01:25: #1 finished! INFO @ Tue, 30 Jun 2020 02:01:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:01:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:01:26: #2 number of paired peaks: 869 WARNING @ Tue, 30 Jun 2020 02:01:26: Fewer paired peaks (869) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 869 pairs to build model! INFO @ Tue, 30 Jun 2020 02:01:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:01:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:01:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:01:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:01:26: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:01:26: #2 alternative fragment length(s) may be 2,16,20 bps INFO @ Tue, 30 Jun 2020 02:01:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.20_model.r WARNING @ Tue, 30 Jun 2020 02:01:26: #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 02:01:26: #2 You may need to consider one of the other alternative d(s): 2,16,20 WARNING @ Tue, 30 Jun 2020 02:01:26: #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 02:01:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:01:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:01:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:01:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:01:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:01:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.10_summits.bed INFO @ Tue, 30 Jun 2020 02:01:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:01:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:02:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:02:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:02:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX182777/SRX182777.20_summits.bed INFO @ Tue, 30 Jun 2020 02:02:13: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling