Job ID = 6529468 SRX = SRX287685 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: 00:09:08 26924228 reads; of these: 26924228 (100.00%) were unpaired; of these: 1437550 (5.34%) aligned 0 times 17200708 (63.89%) aligned exactly 1 time 8285970 (30.78%) aligned >1 times 94.66% overall alignment rate Time searching: 00:09:08 Overall time: 00:09:08 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] 4923010 / 25486678 = 0.1932 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 02:12:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.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 02:12:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:12:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:12:51: 1000000 INFO @ Tue, 30 Jun 2020 02:12:57: 2000000 INFO @ Tue, 30 Jun 2020 02:13:04: 3000000 INFO @ Tue, 30 Jun 2020 02:13:11: 4000000 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 02:13:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.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 02:13:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:13:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:13:18: 5000000 INFO @ Tue, 30 Jun 2020 02:13:22: 1000000 INFO @ Tue, 30 Jun 2020 02:13:26: 6000000 INFO @ Tue, 30 Jun 2020 02:13:29: 2000000 INFO @ Tue, 30 Jun 2020 02:13:33: 7000000 INFO @ Tue, 30 Jun 2020 02:13:36: 3000000 INFO @ Tue, 30 Jun 2020 02:13:41: 8000000 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 02:13:44: 4000000 INFO @ Tue, 30 Jun 2020 02:13:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.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 02:13:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:13:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:13:49: 9000000 INFO @ Tue, 30 Jun 2020 02:13:51: 5000000 INFO @ Tue, 30 Jun 2020 02:13:52: 1000000 INFO @ Tue, 30 Jun 2020 02:13:57: 10000000 INFO @ Tue, 30 Jun 2020 02:13:59: 6000000 INFO @ Tue, 30 Jun 2020 02:13:59: 2000000 INFO @ Tue, 30 Jun 2020 02:14:04: 11000000 INFO @ Tue, 30 Jun 2020 02:14:06: 7000000 INFO @ Tue, 30 Jun 2020 02:14:07: 3000000 INFO @ Tue, 30 Jun 2020 02:14:12: 12000000 INFO @ Tue, 30 Jun 2020 02:14:14: 8000000 INFO @ Tue, 30 Jun 2020 02:14:14: 4000000 INFO @ Tue, 30 Jun 2020 02:14:19: 13000000 INFO @ Tue, 30 Jun 2020 02:14:21: 9000000 INFO @ Tue, 30 Jun 2020 02:14:21: 5000000 INFO @ Tue, 30 Jun 2020 02:14:27: 14000000 INFO @ Tue, 30 Jun 2020 02:14:29: 6000000 INFO @ Tue, 30 Jun 2020 02:14:29: 10000000 INFO @ Tue, 30 Jun 2020 02:14:34: 15000000 INFO @ Tue, 30 Jun 2020 02:14:36: 7000000 INFO @ Tue, 30 Jun 2020 02:14:36: 11000000 INFO @ Tue, 30 Jun 2020 02:14:41: 16000000 INFO @ Tue, 30 Jun 2020 02:14:43: 8000000 INFO @ Tue, 30 Jun 2020 02:14:44: 12000000 INFO @ Tue, 30 Jun 2020 02:14:49: 17000000 INFO @ Tue, 30 Jun 2020 02:14:50: 9000000 INFO @ Tue, 30 Jun 2020 02:14:51: 13000000 INFO @ Tue, 30 Jun 2020 02:14:56: 18000000 INFO @ Tue, 30 Jun 2020 02:14:57: 10000000 INFO @ Tue, 30 Jun 2020 02:14:58: 14000000 INFO @ Tue, 30 Jun 2020 02:15:03: 19000000 INFO @ Tue, 30 Jun 2020 02:15:04: 11000000 INFO @ Tue, 30 Jun 2020 02:15:05: 15000000 INFO @ Tue, 30 Jun 2020 02:15:11: 16000000 INFO @ Tue, 30 Jun 2020 02:15:11: 20000000 INFO @ Tue, 30 Jun 2020 02:15:12: 12000000 INFO @ Tue, 30 Jun 2020 02:15:15: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:15:15: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:15:15: #1 total tags in treatment: 20563668 INFO @ Tue, 30 Jun 2020 02:15:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:15: #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 02:15:16: #1 tags after filtering in treatment: 20563668 INFO @ Tue, 30 Jun 2020 02:15:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:16: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:16: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:17: 17000000 INFO @ Tue, 30 Jun 2020 02:15:18: #2 number of paired peaks: 561 WARNING @ Tue, 30 Jun 2020 02:15:18: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:18: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:18: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:18: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:18: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:18: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:15:18: #2 alternative fragment length(s) may be 1,33,590,595 bps INFO @ Tue, 30 Jun 2020 02:15:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.05_model.r WARNING @ Tue, 30 Jun 2020 02:15:18: #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 02:15:18: #2 You may need to consider one of the other alternative d(s): 1,33,590,595 WARNING @ Tue, 30 Jun 2020 02:15:18: #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 02:15:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:15:19: 13000000 INFO @ Tue, 30 Jun 2020 02:15:23: 18000000 INFO @ Tue, 30 Jun 2020 02:15:25: 14000000 INFO @ Tue, 30 Jun 2020 02:15:29: 19000000 INFO @ Tue, 30 Jun 2020 02:15:32: 15000000 INFO @ Tue, 30 Jun 2020 02:15:35: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:15:38: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:15:38: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:15:38: #1 total tags in treatment: 20563668 INFO @ Tue, 30 Jun 2020 02:15:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:38: #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 02:15:39: #1 tags after filtering in treatment: 20563668 INFO @ Tue, 30 Jun 2020 02:15:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:39: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:39: 16000000 INFO @ Tue, 30 Jun 2020 02:15:41: #2 number of paired peaks: 561 WARNING @ Tue, 30 Jun 2020 02:15:41: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:41: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:41: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:41: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:41: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:41: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:15:41: #2 alternative fragment length(s) may be 1,33,590,595 bps INFO @ Tue, 30 Jun 2020 02:15:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.10_model.r WARNING @ Tue, 30 Jun 2020 02:15:41: #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 02:15:41: #2 You may need to consider one of the other alternative d(s): 1,33,590,595 WARNING @ Tue, 30 Jun 2020 02:15:41: #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 02:15:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:15:47: 17000000 INFO @ Tue, 30 Jun 2020 02:15:49: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:15:54: 18000000 INFO @ Tue, 30 Jun 2020 02:15:59: 19000000 INFO @ Tue, 30 Jun 2020 02:16:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.05_summits.bed INFO @ Tue, 30 Jun 2020 02:16:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:16:05: 20000000 INFO @ Tue, 30 Jun 2020 02:16:09: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:16:09: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:16:09: #1 total tags in treatment: 20563668 INFO @ Tue, 30 Jun 2020 02:16:09: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:16:09: #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 02:16:10: #1 tags after filtering in treatment: 20563668 INFO @ Tue, 30 Jun 2020 02:16:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:16:10: #1 finished! INFO @ Tue, 30 Jun 2020 02:16:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:16:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:16:11: #2 number of paired peaks: 561 WARNING @ Tue, 30 Jun 2020 02:16:11: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Tue, 30 Jun 2020 02:16:11: start model_add_line... INFO @ Tue, 30 Jun 2020 02:16:11: start X-correlation... INFO @ Tue, 30 Jun 2020 02:16:11: end of X-cor INFO @ Tue, 30 Jun 2020 02:16:11: #2 finished! INFO @ Tue, 30 Jun 2020 02:16:11: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:16:11: #2 alternative fragment length(s) may be 1,33,590,595 bps INFO @ Tue, 30 Jun 2020 02:16:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.20_model.r WARNING @ Tue, 30 Jun 2020 02:16:11: #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 02:16:11: #2 You may need to consider one of the other alternative d(s): 1,33,590,595 WARNING @ Tue, 30 Jun 2020 02:16:11: #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 02:16:11: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:16:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:16:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:16:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.10_summits.bed INFO @ Tue, 30 Jun 2020 02:16:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:16:43: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:16:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287685/SRX287685.20_summits.bed INFO @ Tue, 30 Jun 2020 02:16:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling