Job ID = 6627071 SRX = SRX7780045 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: 00:04:36 16249120 reads; of these: 16249120 (100.00%) were unpaired; of these: 1404274 (8.64%) aligned 0 times 10741203 (66.10%) aligned exactly 1 time 4103643 (25.25%) aligned >1 times 91.36% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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] 2766572 / 14844846 = 0.1864 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, 14 Jul 2020 09:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.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, 14 Jul 2020 09:53:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:53:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:53:20: 1000000 INFO @ Tue, 14 Jul 2020 09:53:26: 2000000 INFO @ Tue, 14 Jul 2020 09:53:32: 3000000 INFO @ Tue, 14 Jul 2020 09:53:37: 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, 14 Jul 2020 09:53:43: 5000000 INFO @ Tue, 14 Jul 2020 09:53:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.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, 14 Jul 2020 09:53:44: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:53:44: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:53:49: 6000000 INFO @ Tue, 14 Jul 2020 09:53:50: 1000000 INFO @ Tue, 14 Jul 2020 09:53:55: 7000000 INFO @ Tue, 14 Jul 2020 09:53:55: 2000000 INFO @ Tue, 14 Jul 2020 09:54:01: 3000000 INFO @ Tue, 14 Jul 2020 09:54:01: 8000000 INFO @ Tue, 14 Jul 2020 09:54:06: 4000000 INFO @ Tue, 14 Jul 2020 09:54:07: 9000000 INFO @ Tue, 14 Jul 2020 09:54:12: 5000000 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, 14 Jul 2020 09:54:13: 10000000 INFO @ Tue, 14 Jul 2020 09:54:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.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, 14 Jul 2020 09:54:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:54:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:54:17: 6000000 INFO @ Tue, 14 Jul 2020 09:54:19: 11000000 INFO @ Tue, 14 Jul 2020 09:54:20: 1000000 INFO @ Tue, 14 Jul 2020 09:54:22: 7000000 INFO @ Tue, 14 Jul 2020 09:54:25: 2000000 INFO @ Tue, 14 Jul 2020 09:54:26: 12000000 INFO @ Tue, 14 Jul 2020 09:54:26: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 09:54:26: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 09:54:26: #1 total tags in treatment: 12078274 INFO @ Tue, 14 Jul 2020 09:54:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:54:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:54:27: #1 tags after filtering in treatment: 12078190 INFO @ Tue, 14 Jul 2020 09:54:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:54:27: #1 finished! INFO @ Tue, 14 Jul 2020 09:54:27: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:54:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:54:27: #2 number of paired peaks: 151 WARNING @ Tue, 14 Jul 2020 09:54:27: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Tue, 14 Jul 2020 09:54:27: start model_add_line... INFO @ Tue, 14 Jul 2020 09:54:27: start X-correlation... INFO @ Tue, 14 Jul 2020 09:54:27: end of X-cor INFO @ Tue, 14 Jul 2020 09:54:27: #2 finished! INFO @ Tue, 14 Jul 2020 09:54:27: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 09:54:27: #2 alternative fragment length(s) may be 3,25,53,580 bps INFO @ Tue, 14 Jul 2020 09:54:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.05_model.r WARNING @ Tue, 14 Jul 2020 09:54:27: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:54:27: #2 You may need to consider one of the other alternative d(s): 3,25,53,580 WARNING @ Tue, 14 Jul 2020 09:54:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:54:27: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:54:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:54:28: 8000000 INFO @ Tue, 14 Jul 2020 09:54:31: 3000000 INFO @ Tue, 14 Jul 2020 09:54:33: 9000000 INFO @ Tue, 14 Jul 2020 09:54:36: 4000000 INFO @ Tue, 14 Jul 2020 09:54:39: 10000000 INFO @ Tue, 14 Jul 2020 09:54:41: 5000000 INFO @ Tue, 14 Jul 2020 09:54:46: 11000000 INFO @ Tue, 14 Jul 2020 09:54:47: 6000000 INFO @ Tue, 14 Jul 2020 09:54:51: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:54:52: 7000000 INFO @ Tue, 14 Jul 2020 09:54:54: 12000000 INFO @ Tue, 14 Jul 2020 09:54:54: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 09:54:54: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 09:54:54: #1 total tags in treatment: 12078274 INFO @ Tue, 14 Jul 2020 09:54:54: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:54:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:54:55: #1 tags after filtering in treatment: 12078190 INFO @ Tue, 14 Jul 2020 09:54:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:54:55: #1 finished! INFO @ Tue, 14 Jul 2020 09:54:55: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:54:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:54:56: #2 number of paired peaks: 151 WARNING @ Tue, 14 Jul 2020 09:54:56: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Tue, 14 Jul 2020 09:54:56: start model_add_line... INFO @ Tue, 14 Jul 2020 09:54:56: start X-correlation... INFO @ Tue, 14 Jul 2020 09:54:56: end of X-cor INFO @ Tue, 14 Jul 2020 09:54:56: #2 finished! INFO @ Tue, 14 Jul 2020 09:54:56: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 09:54:56: #2 alternative fragment length(s) may be 3,25,53,580 bps INFO @ Tue, 14 Jul 2020 09:54:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.10_model.r WARNING @ Tue, 14 Jul 2020 09:54:56: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:54:56: #2 You may need to consider one of the other alternative d(s): 3,25,53,580 WARNING @ Tue, 14 Jul 2020 09:54:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:54:56: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:54:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:54:58: 8000000 INFO @ Tue, 14 Jul 2020 09:55:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:55:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:55:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.05_summits.bed INFO @ Tue, 14 Jul 2020 09:55:02: Done! pass1 - making usageList (412 chroms): 1 millis pass2 - checking and writing primary data (1155 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:55:03: 9000000 INFO @ Tue, 14 Jul 2020 09:55:08: 10000000 INFO @ Tue, 14 Jul 2020 09:55:14: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:55:19: 12000000 INFO @ Tue, 14 Jul 2020 09:55:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:55:19: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 09:55:19: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 09:55:19: #1 total tags in treatment: 12078274 INFO @ Tue, 14 Jul 2020 09:55:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:55:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:55:20: #1 tags after filtering in treatment: 12078190 INFO @ Tue, 14 Jul 2020 09:55:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:55:20: #1 finished! INFO @ Tue, 14 Jul 2020 09:55:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:55:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:55:21: #2 number of paired peaks: 151 WARNING @ Tue, 14 Jul 2020 09:55:21: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Tue, 14 Jul 2020 09:55:21: start model_add_line... INFO @ Tue, 14 Jul 2020 09:55:21: start X-correlation... INFO @ Tue, 14 Jul 2020 09:55:21: end of X-cor INFO @ Tue, 14 Jul 2020 09:55:21: #2 finished! INFO @ Tue, 14 Jul 2020 09:55:21: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 09:55:21: #2 alternative fragment length(s) may be 3,25,53,580 bps INFO @ Tue, 14 Jul 2020 09:55:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.20_model.r WARNING @ Tue, 14 Jul 2020 09:55:21: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:55:21: #2 You may need to consider one of the other alternative d(s): 3,25,53,580 WARNING @ Tue, 14 Jul 2020 09:55:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:55:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:55:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:55:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:55:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:55:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.10_summits.bed INFO @ Tue, 14 Jul 2020 09:55:30: Done! pass1 - making usageList (150 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:55:44: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:55:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:55:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:55:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7780045/SRX7780045.20_summits.bed INFO @ Tue, 14 Jul 2020 09:55:55: Done! pass1 - making usageList (34 chroms): 0 millis pass2 - checking and writing primary data (59 records, 4 fields): 3 millis CompletedMACS2peakCalling