Job ID = 6529183 SRX = SRX032119 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: 00:07:54 24896839 reads; of these: 24896839 (100.00%) were unpaired; of these: 352163 (1.41%) aligned 0 times 16072540 (64.56%) aligned exactly 1 time 8472136 (34.03%) aligned >1 times 98.59% overall alignment rate Time searching: 00:07:54 Overall time: 00:07:54 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] 6944143 / 24544676 = 0.2829 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 01:49:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.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 01:49:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:49:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:49:29: 1000000 INFO @ Tue, 30 Jun 2020 01:49:34: 2000000 INFO @ Tue, 30 Jun 2020 01:49:39: 3000000 INFO @ Tue, 30 Jun 2020 01:49:43: 4000000 INFO @ Tue, 30 Jun 2020 01:49:48: 5000000 INFO @ Tue, 30 Jun 2020 01:49:52: 6000000 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 01:49:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.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 01:49:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:49:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:49:57: 7000000 INFO @ Tue, 30 Jun 2020 01:49:59: 1000000 INFO @ Tue, 30 Jun 2020 01:50:01: 8000000 INFO @ Tue, 30 Jun 2020 01:50:04: 2000000 INFO @ Tue, 30 Jun 2020 01:50:06: 9000000 INFO @ Tue, 30 Jun 2020 01:50:09: 3000000 INFO @ Tue, 30 Jun 2020 01:50:11: 10000000 INFO @ Tue, 30 Jun 2020 01:50:13: 4000000 INFO @ Tue, 30 Jun 2020 01:50:15: 11000000 INFO @ Tue, 30 Jun 2020 01:50:18: 5000000 INFO @ Tue, 30 Jun 2020 01:50:20: 12000000 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 01:50:22: 6000000 INFO @ Tue, 30 Jun 2020 01:50:24: 13000000 INFO @ Tue, 30 Jun 2020 01:50:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.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 01:50:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:50:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:50:27: 7000000 INFO @ Tue, 30 Jun 2020 01:50:30: 1000000 INFO @ Tue, 30 Jun 2020 01:50:30: 14000000 INFO @ Tue, 30 Jun 2020 01:50:32: 8000000 INFO @ Tue, 30 Jun 2020 01:50:35: 15000000 INFO @ Tue, 30 Jun 2020 01:50:35: 2000000 INFO @ Tue, 30 Jun 2020 01:50:37: 9000000 INFO @ Tue, 30 Jun 2020 01:50:39: 16000000 INFO @ Tue, 30 Jun 2020 01:50:40: 3000000 INFO @ Tue, 30 Jun 2020 01:50:43: 10000000 INFO @ Tue, 30 Jun 2020 01:50:44: 17000000 INFO @ Tue, 30 Jun 2020 01:50:45: 4000000 INFO @ Tue, 30 Jun 2020 01:50:47: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:50:47: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:50:47: #1 total tags in treatment: 17600533 INFO @ Tue, 30 Jun 2020 01:50:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:50:47: #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 01:50:48: 11000000 INFO @ Tue, 30 Jun 2020 01:50:48: #1 tags after filtering in treatment: 17600488 INFO @ Tue, 30 Jun 2020 01:50:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:50:48: #1 finished! INFO @ Tue, 30 Jun 2020 01:50:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:50:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:50:50: #2 number of paired peaks: 779 WARNING @ Tue, 30 Jun 2020 01:50:50: Fewer paired peaks (779) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 779 pairs to build model! INFO @ Tue, 30 Jun 2020 01:50:50: start model_add_line... INFO @ Tue, 30 Jun 2020 01:50:50: start X-correlation... INFO @ Tue, 30 Jun 2020 01:50:50: end of X-cor INFO @ Tue, 30 Jun 2020 01:50:50: #2 finished! INFO @ Tue, 30 Jun 2020 01:50:50: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:50:50: #2 alternative fragment length(s) may be 1 bps INFO @ Tue, 30 Jun 2020 01:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.05_model.r WARNING @ Tue, 30 Jun 2020 01:50:50: #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 01:50:50: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Tue, 30 Jun 2020 01:50:50: #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 01:50:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:50:50: 5000000 INFO @ Tue, 30 Jun 2020 01:50:53: 12000000 INFO @ Tue, 30 Jun 2020 01:50:55: 6000000 INFO @ Tue, 30 Jun 2020 01:50:58: 13000000 INFO @ Tue, 30 Jun 2020 01:51:00: 7000000 INFO @ Tue, 30 Jun 2020 01:51:04: 14000000 INFO @ Tue, 30 Jun 2020 01:51:05: 8000000 INFO @ Tue, 30 Jun 2020 01:51:09: 15000000 INFO @ Tue, 30 Jun 2020 01:51:10: 9000000 INFO @ Tue, 30 Jun 2020 01:51:14: 16000000 INFO @ Tue, 30 Jun 2020 01:51:15: 10000000 INFO @ Tue, 30 Jun 2020 01:51:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:51:19: 17000000 INFO @ Tue, 30 Jun 2020 01:51:20: 11000000 INFO @ Tue, 30 Jun 2020 01:51:22: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:51:22: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:51:22: #1 total tags in treatment: 17600533 INFO @ Tue, 30 Jun 2020 01:51:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:51:22: #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 01:51:23: #1 tags after filtering in treatment: 17600488 INFO @ Tue, 30 Jun 2020 01:51:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:51:23: #1 finished! INFO @ Tue, 30 Jun 2020 01:51:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:51:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:51:24: #2 number of paired peaks: 779 WARNING @ Tue, 30 Jun 2020 01:51:24: Fewer paired peaks (779) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 779 pairs to build model! INFO @ Tue, 30 Jun 2020 01:51:24: start model_add_line... INFO @ Tue, 30 Jun 2020 01:51:24: 12000000 INFO @ Tue, 30 Jun 2020 01:51:25: start X-correlation... INFO @ Tue, 30 Jun 2020 01:51:25: end of X-cor INFO @ Tue, 30 Jun 2020 01:51:25: #2 finished! INFO @ Tue, 30 Jun 2020 01:51:25: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:51:25: #2 alternative fragment length(s) may be 1 bps INFO @ Tue, 30 Jun 2020 01:51:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.10_model.r WARNING @ Tue, 30 Jun 2020 01:51:25: #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 01:51:25: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Tue, 30 Jun 2020 01:51:25: #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 01:51:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:51:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:51:29: 13000000 INFO @ Tue, 30 Jun 2020 01:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.05_summits.bed INFO @ Tue, 30 Jun 2020 01:51:31: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:51:34: 14000000 INFO @ Tue, 30 Jun 2020 01:51:39: 15000000 INFO @ Tue, 30 Jun 2020 01:51:43: 16000000 INFO @ Tue, 30 Jun 2020 01:51:47: 17000000 INFO @ Tue, 30 Jun 2020 01:51:51: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:51:51: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:51:51: #1 total tags in treatment: 17600533 INFO @ Tue, 30 Jun 2020 01:51:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:51:51: #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 01:51:51: #1 tags after filtering in treatment: 17600488 INFO @ Tue, 30 Jun 2020 01:51:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:51:51: #1 finished! INFO @ Tue, 30 Jun 2020 01:51:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:51:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:51:53: #2 number of paired peaks: 779 WARNING @ Tue, 30 Jun 2020 01:51:53: Fewer paired peaks (779) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 779 pairs to build model! INFO @ Tue, 30 Jun 2020 01:51:53: start model_add_line... INFO @ Tue, 30 Jun 2020 01:51:53: start X-correlation... INFO @ Tue, 30 Jun 2020 01:51:53: end of X-cor INFO @ Tue, 30 Jun 2020 01:51:53: #2 finished! INFO @ Tue, 30 Jun 2020 01:51:53: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 01:51:53: #2 alternative fragment length(s) may be 1 bps INFO @ Tue, 30 Jun 2020 01:51:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.20_model.r WARNING @ Tue, 30 Jun 2020 01:51:53: #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 01:51:53: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Tue, 30 Jun 2020 01:51:53: #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 01:51:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:51:53: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:52:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:52:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:52:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.10_summits.bed INFO @ Tue, 30 Jun 2020 01:52:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:52:20: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:52:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:52:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:52:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX032119/SRX032119.20_summits.bed INFO @ Tue, 30 Jun 2020 01:52:34: 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。