Job ID = 6529785 SRX = SRX481092 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: 00:06:25 22109731 reads; of these: 22109731 (100.00%) were unpaired; of these: 1594131 (7.21%) aligned 0 times 13930092 (63.00%) aligned exactly 1 time 6585508 (29.79%) aligned >1 times 92.79% overall alignment rate Time searching: 00:06:25 Overall time: 00:06:25 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] 4221065 / 20515600 = 0.2057 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 02:52:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.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 02:52:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:58: 1000000 INFO @ Tue, 30 Jun 2020 02:53:04: 2000000 INFO @ Tue, 30 Jun 2020 02:53:10: 3000000 INFO @ Tue, 30 Jun 2020 02:53:15: 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 02:53:21: 5000000 INFO @ Tue, 30 Jun 2020 02:53:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.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 02:53:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:53:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:53:27: 6000000 INFO @ Tue, 30 Jun 2020 02:53:28: 1000000 INFO @ Tue, 30 Jun 2020 02:53:33: 7000000 INFO @ Tue, 30 Jun 2020 02:53:34: 2000000 INFO @ Tue, 30 Jun 2020 02:53:39: 8000000 INFO @ Tue, 30 Jun 2020 02:53:40: 3000000 INFO @ Tue, 30 Jun 2020 02:53:44: 9000000 INFO @ Tue, 30 Jun 2020 02:53:45: 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 02:53:50: 10000000 INFO @ Tue, 30 Jun 2020 02:53:51: 5000000 INFO @ Tue, 30 Jun 2020 02:53:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.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 02:53:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:53:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:53:56: 11000000 INFO @ Tue, 30 Jun 2020 02:53:57: 6000000 INFO @ Tue, 30 Jun 2020 02:53:59: 1000000 INFO @ Tue, 30 Jun 2020 02:54:02: 12000000 INFO @ Tue, 30 Jun 2020 02:54:03: 7000000 INFO @ Tue, 30 Jun 2020 02:54:06: 2000000 INFO @ Tue, 30 Jun 2020 02:54:09: 13000000 INFO @ Tue, 30 Jun 2020 02:54:09: 8000000 INFO @ Tue, 30 Jun 2020 02:54:13: 3000000 INFO @ Tue, 30 Jun 2020 02:54:15: 9000000 INFO @ Tue, 30 Jun 2020 02:54:15: 14000000 INFO @ Tue, 30 Jun 2020 02:54:19: 4000000 INFO @ Tue, 30 Jun 2020 02:54:20: 10000000 INFO @ Tue, 30 Jun 2020 02:54:21: 15000000 INFO @ Tue, 30 Jun 2020 02:54:26: 11000000 INFO @ Tue, 30 Jun 2020 02:54:27: 5000000 INFO @ Tue, 30 Jun 2020 02:54:27: 16000000 INFO @ Tue, 30 Jun 2020 02:54:29: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:54:29: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:54:29: #1 total tags in treatment: 16294535 INFO @ Tue, 30 Jun 2020 02:54:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:54:29: #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 02:54:30: #1 tags after filtering in treatment: 16294535 INFO @ Tue, 30 Jun 2020 02:54:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:54:30: #1 finished! INFO @ Tue, 30 Jun 2020 02:54:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:54:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:54:31: #2 number of paired peaks: 698 WARNING @ Tue, 30 Jun 2020 02:54:31: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Tue, 30 Jun 2020 02:54:31: start model_add_line... INFO @ Tue, 30 Jun 2020 02:54:31: start X-correlation... INFO @ Tue, 30 Jun 2020 02:54:31: end of X-cor INFO @ Tue, 30 Jun 2020 02:54:31: #2 finished! INFO @ Tue, 30 Jun 2020 02:54:31: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:54:31: #2 alternative fragment length(s) may be 2,31 bps INFO @ Tue, 30 Jun 2020 02:54:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.05_model.r WARNING @ Tue, 30 Jun 2020 02:54:31: #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 02:54:31: #2 You may need to consider one of the other alternative d(s): 2,31 WARNING @ Tue, 30 Jun 2020 02:54:31: #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 02:54:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:54:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:54:32: 12000000 INFO @ Tue, 30 Jun 2020 02:54:34: 6000000 INFO @ Tue, 30 Jun 2020 02:54:39: 13000000 INFO @ Tue, 30 Jun 2020 02:54:41: 7000000 INFO @ Tue, 30 Jun 2020 02:54:45: 14000000 INFO @ Tue, 30 Jun 2020 02:54:47: 8000000 INFO @ Tue, 30 Jun 2020 02:54:51: 15000000 INFO @ Tue, 30 Jun 2020 02:54:53: 9000000 INFO @ Tue, 30 Jun 2020 02:54:57: 16000000 INFO @ Tue, 30 Jun 2020 02:54:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:54:59: 10000000 INFO @ Tue, 30 Jun 2020 02:54:59: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:54:59: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:54:59: #1 total tags in treatment: 16294535 INFO @ Tue, 30 Jun 2020 02:54:59: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:54:59: #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 02:55:00: #1 tags after filtering in treatment: 16294535 INFO @ Tue, 30 Jun 2020 02:55:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:55:00: #1 finished! INFO @ Tue, 30 Jun 2020 02:55:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:55:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:55:01: #2 number of paired peaks: 698 WARNING @ Tue, 30 Jun 2020 02:55:01: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Tue, 30 Jun 2020 02:55:01: start model_add_line... INFO @ Tue, 30 Jun 2020 02:55:01: start X-correlation... INFO @ Tue, 30 Jun 2020 02:55:01: end of X-cor INFO @ Tue, 30 Jun 2020 02:55:01: #2 finished! INFO @ Tue, 30 Jun 2020 02:55:01: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:55:01: #2 alternative fragment length(s) may be 2,31 bps INFO @ Tue, 30 Jun 2020 02:55:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.10_model.r WARNING @ Tue, 30 Jun 2020 02:55:01: #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 02:55:01: #2 You may need to consider one of the other alternative d(s): 2,31 WARNING @ Tue, 30 Jun 2020 02:55:01: #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 02:55:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:55:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:55:05: 11000000 INFO @ Tue, 30 Jun 2020 02:55:11: 12000000 INFO @ Tue, 30 Jun 2020 02:55:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:55:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:55:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.05_summits.bed INFO @ Tue, 30 Jun 2020 02:55:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:55:17: 13000000 INFO @ Tue, 30 Jun 2020 02:55:23: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:55:28: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:55:29: 15000000 INFO @ Tue, 30 Jun 2020 02:55:35: 16000000 INFO @ Tue, 30 Jun 2020 02:55:37: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:55:37: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:55:37: #1 total tags in treatment: 16294535 INFO @ Tue, 30 Jun 2020 02:55:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:55:37: #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 02:55:37: #1 tags after filtering in treatment: 16294535 INFO @ Tue, 30 Jun 2020 02:55:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:55:37: #1 finished! INFO @ Tue, 30 Jun 2020 02:55:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:55:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:55:39: #2 number of paired peaks: 698 WARNING @ Tue, 30 Jun 2020 02:55:39: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Tue, 30 Jun 2020 02:55:39: start model_add_line... INFO @ Tue, 30 Jun 2020 02:55:39: start X-correlation... INFO @ Tue, 30 Jun 2020 02:55:39: end of X-cor INFO @ Tue, 30 Jun 2020 02:55:39: #2 finished! INFO @ Tue, 30 Jun 2020 02:55:39: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:55:39: #2 alternative fragment length(s) may be 2,31 bps INFO @ Tue, 30 Jun 2020 02:55:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.20_model.r WARNING @ Tue, 30 Jun 2020 02:55:39: #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 02:55:39: #2 You may need to consider one of the other alternative d(s): 2,31 WARNING @ Tue, 30 Jun 2020 02:55:39: #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 02:55:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:55:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:55:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:55:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:55:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.10_summits.bed INFO @ Tue, 30 Jun 2020 02:55:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:56:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:56:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:56:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:56:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX481092/SRX481092.20_summits.bed INFO @ Tue, 30 Jun 2020 02:56:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling