Job ID = 6529484 SRX = SRX287773 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: 00:08:32 26924228 reads; of these: 26924228 (100.00%) were unpaired; of these: 1437591 (5.34%) aligned 0 times 17200567 (63.89%) aligned exactly 1 time 8286070 (30.78%) aligned >1 times 94.66% overall alignment rate Time searching: 00:08:32 Overall time: 00:08:32 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] 4922974 / 25486637 = 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 02:23:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.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 02:23:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:23:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:23:45: 1000000 INFO @ Tue, 30 Jun 2020 02:23:50: 2000000 INFO @ Tue, 30 Jun 2020 02:23:56: 3000000 INFO @ Tue, 30 Jun 2020 02:24:01: 4000000 INFO @ Tue, 30 Jun 2020 02:24:06: 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 02:24:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.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 02:24:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:24:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:24:11: 6000000 INFO @ Tue, 30 Jun 2020 02:24:17: 1000000 INFO @ Tue, 30 Jun 2020 02:24:17: 7000000 INFO @ Tue, 30 Jun 2020 02:24:23: 8000000 INFO @ Tue, 30 Jun 2020 02:24:23: 2000000 INFO @ Tue, 30 Jun 2020 02:24:29: 9000000 INFO @ Tue, 30 Jun 2020 02:24:30: 3000000 INFO @ Tue, 30 Jun 2020 02:24:35: 10000000 INFO @ Tue, 30 Jun 2020 02:24:36: 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 02:24:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.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 02:24:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:24:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:24:41: 11000000 INFO @ Tue, 30 Jun 2020 02:24:43: 5000000 INFO @ Tue, 30 Jun 2020 02:24:46: 1000000 INFO @ Tue, 30 Jun 2020 02:24:47: 12000000 INFO @ Tue, 30 Jun 2020 02:24:49: 6000000 INFO @ Tue, 30 Jun 2020 02:24:52: 2000000 INFO @ Tue, 30 Jun 2020 02:24:53: 13000000 INFO @ Tue, 30 Jun 2020 02:24:56: 7000000 INFO @ Tue, 30 Jun 2020 02:24:58: 3000000 INFO @ Tue, 30 Jun 2020 02:24:59: 14000000 INFO @ Tue, 30 Jun 2020 02:25:03: 8000000 INFO @ Tue, 30 Jun 2020 02:25:04: 4000000 INFO @ Tue, 30 Jun 2020 02:25:05: 15000000 INFO @ Tue, 30 Jun 2020 02:25:09: 9000000 INFO @ Tue, 30 Jun 2020 02:25:10: 5000000 INFO @ Tue, 30 Jun 2020 02:25:11: 16000000 INFO @ Tue, 30 Jun 2020 02:25:16: 10000000 INFO @ Tue, 30 Jun 2020 02:25:16: 6000000 INFO @ Tue, 30 Jun 2020 02:25:17: 17000000 INFO @ Tue, 30 Jun 2020 02:25:22: 7000000 INFO @ Tue, 30 Jun 2020 02:25:23: 11000000 INFO @ Tue, 30 Jun 2020 02:25:23: 18000000 INFO @ Tue, 30 Jun 2020 02:25:29: 8000000 INFO @ Tue, 30 Jun 2020 02:25:29: 12000000 INFO @ Tue, 30 Jun 2020 02:25:29: 19000000 INFO @ Tue, 30 Jun 2020 02:25:35: 9000000 INFO @ Tue, 30 Jun 2020 02:25:36: 13000000 INFO @ Tue, 30 Jun 2020 02:25:36: 20000000 INFO @ Tue, 30 Jun 2020 02:25:39: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:25:39: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:25:39: #1 total tags in treatment: 20563663 INFO @ Tue, 30 Jun 2020 02:25:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:25:39: #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 02:25:40: #1 tags after filtering in treatment: 20563663 INFO @ Tue, 30 Jun 2020 02:25:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:25:40: #1 finished! INFO @ Tue, 30 Jun 2020 02:25:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:25:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:25:41: 10000000 INFO @ Tue, 30 Jun 2020 02:25:41: #2 number of paired peaks: 573 WARNING @ Tue, 30 Jun 2020 02:25:41: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Tue, 30 Jun 2020 02:25:41: start model_add_line... INFO @ Tue, 30 Jun 2020 02:25:41: start X-correlation... INFO @ Tue, 30 Jun 2020 02:25:41: end of X-cor INFO @ Tue, 30 Jun 2020 02:25:41: #2 finished! INFO @ Tue, 30 Jun 2020 02:25:41: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:25:41: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 30 Jun 2020 02:25:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.05_model.r WARNING @ Tue, 30 Jun 2020 02:25:41: #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 02:25:41: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 30 Jun 2020 02:25:41: #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 02:25:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:25:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:25:42: 14000000 INFO @ Tue, 30 Jun 2020 02:25:47: 11000000 INFO @ Tue, 30 Jun 2020 02:25:48: 15000000 INFO @ Tue, 30 Jun 2020 02:25:53: 12000000 INFO @ Tue, 30 Jun 2020 02:25:55: 16000000 INFO @ Tue, 30 Jun 2020 02:25:59: 13000000 INFO @ Tue, 30 Jun 2020 02:26:02: 17000000 INFO @ Tue, 30 Jun 2020 02:26:05: 14000000 INFO @ Tue, 30 Jun 2020 02:26:09: 18000000 INFO @ Tue, 30 Jun 2020 02:26:11: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:26:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:26:15: 19000000 INFO @ Tue, 30 Jun 2020 02:26:17: 16000000 INFO @ Tue, 30 Jun 2020 02:26:22: 20000000 INFO @ Tue, 30 Jun 2020 02:26:23: 17000000 INFO @ Tue, 30 Jun 2020 02:26:26: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:26:26: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:26:26: #1 total tags in treatment: 20563663 INFO @ Tue, 30 Jun 2020 02:26:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:26:26: #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 02:26:26: #1 tags after filtering in treatment: 20563663 INFO @ Tue, 30 Jun 2020 02:26:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:26:26: #1 finished! INFO @ Tue, 30 Jun 2020 02:26:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:26:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:26:28: #2 number of paired peaks: 573 WARNING @ Tue, 30 Jun 2020 02:26:28: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Tue, 30 Jun 2020 02:26:28: start model_add_line... INFO @ Tue, 30 Jun 2020 02:26:28: start X-correlation... INFO @ Tue, 30 Jun 2020 02:26:28: end of X-cor INFO @ Tue, 30 Jun 2020 02:26:28: #2 finished! INFO @ Tue, 30 Jun 2020 02:26:28: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:26:28: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 30 Jun 2020 02:26:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.10_model.r WARNING @ Tue, 30 Jun 2020 02:26:28: #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 02:26:28: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 30 Jun 2020 02:26:28: #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 02:26:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:26:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:26:29: 18000000 INFO @ Tue, 30 Jun 2020 02:26:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:26:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:26:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.05_summits.bed INFO @ Tue, 30 Jun 2020 02:26:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:26:35: 19000000 INFO @ Tue, 30 Jun 2020 02:26:40: 20000000 INFO @ Tue, 30 Jun 2020 02:26:44: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:26:44: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:26:44: #1 total tags in treatment: 20563663 INFO @ Tue, 30 Jun 2020 02:26:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:26:44: #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 02:26:44: #1 tags after filtering in treatment: 20563663 INFO @ Tue, 30 Jun 2020 02:26:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:26:44: #1 finished! INFO @ Tue, 30 Jun 2020 02:26:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:26:46: #2 number of paired peaks: 573 WARNING @ Tue, 30 Jun 2020 02:26:46: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Tue, 30 Jun 2020 02:26:46: start model_add_line... INFO @ Tue, 30 Jun 2020 02:26:46: start X-correlation... INFO @ Tue, 30 Jun 2020 02:26:46: end of X-cor INFO @ Tue, 30 Jun 2020 02:26:46: #2 finished! INFO @ Tue, 30 Jun 2020 02:26:46: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:26:46: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 30 Jun 2020 02:26:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.20_model.r WARNING @ Tue, 30 Jun 2020 02:26:46: #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 02:26:46: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 30 Jun 2020 02:26:46: #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 02:26:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:26:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:27:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:27:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:27:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:27:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.10_summits.bed INFO @ Tue, 30 Jun 2020 02:27:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:27:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:27:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:27:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:27:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287773/SRX287773.20_summits.bed INFO @ Tue, 30 Jun 2020 02:27:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling