Job ID = 6529338 SRX = SRX1847050 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: 00:10:19 36399187 reads; of these: 36399187 (100.00%) were unpaired; of these: 1283603 (3.53%) aligned 0 times 24101402 (66.21%) aligned exactly 1 time 11014182 (30.26%) aligned >1 times 96.47% overall alignment rate Time searching: 00:10:19 Overall time: 00:10:19 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 16 files... [bam_rmdupse_core] 14309309 / 35115584 = 0.4075 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 02:05:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.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 02:05:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:05:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:05:17: 1000000 INFO @ Tue, 30 Jun 2020 02:05:22: 2000000 INFO @ Tue, 30 Jun 2020 02:05:27: 3000000 INFO @ Tue, 30 Jun 2020 02:05:32: 4000000 INFO @ Tue, 30 Jun 2020 02:05:37: 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 02:05:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.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 02:05:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:05:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:05:42: 6000000 INFO @ Tue, 30 Jun 2020 02:05:48: 1000000 INFO @ Tue, 30 Jun 2020 02:05:48: 7000000 INFO @ Tue, 30 Jun 2020 02:05:53: 2000000 INFO @ Tue, 30 Jun 2020 02:05:53: 8000000 INFO @ Tue, 30 Jun 2020 02:05:59: 3000000 INFO @ Tue, 30 Jun 2020 02:05:59: 9000000 INFO @ Tue, 30 Jun 2020 02:06:04: 4000000 INFO @ Tue, 30 Jun 2020 02:06:04: 10000000 INFO @ Tue, 30 Jun 2020 02:06:10: 5000000 INFO @ Tue, 30 Jun 2020 02:06:10: 11000000 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 02:06:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.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 02:06:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:06:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:06:15: 12000000 INFO @ Tue, 30 Jun 2020 02:06:15: 6000000 INFO @ Tue, 30 Jun 2020 02:06:19: 1000000 INFO @ Tue, 30 Jun 2020 02:06:21: 13000000 INFO @ Tue, 30 Jun 2020 02:06:21: 7000000 INFO @ Tue, 30 Jun 2020 02:06:25: 2000000 INFO @ Tue, 30 Jun 2020 02:06:27: 14000000 INFO @ Tue, 30 Jun 2020 02:06:27: 8000000 INFO @ Tue, 30 Jun 2020 02:06:32: 3000000 INFO @ Tue, 30 Jun 2020 02:06:33: 15000000 INFO @ Tue, 30 Jun 2020 02:06:33: 9000000 INFO @ Tue, 30 Jun 2020 02:06:38: 4000000 INFO @ Tue, 30 Jun 2020 02:06:39: 16000000 INFO @ Tue, 30 Jun 2020 02:06:39: 10000000 INFO @ Tue, 30 Jun 2020 02:06:44: 11000000 INFO @ Tue, 30 Jun 2020 02:06:45: 17000000 INFO @ Tue, 30 Jun 2020 02:06:45: 5000000 INFO @ Tue, 30 Jun 2020 02:06:50: 12000000 INFO @ Tue, 30 Jun 2020 02:06:50: 18000000 INFO @ Tue, 30 Jun 2020 02:06:51: 6000000 INFO @ Tue, 30 Jun 2020 02:06:56: 13000000 INFO @ Tue, 30 Jun 2020 02:06:56: 19000000 INFO @ Tue, 30 Jun 2020 02:06:58: 7000000 INFO @ Tue, 30 Jun 2020 02:07:02: 14000000 INFO @ Tue, 30 Jun 2020 02:07:02: 20000000 INFO @ Tue, 30 Jun 2020 02:07:04: 8000000 INFO @ Tue, 30 Jun 2020 02:07:07: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:07:07: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:07:07: #1 total tags in treatment: 20806275 INFO @ Tue, 30 Jun 2020 02:07:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:07:07: #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 02:07:07: 15000000 INFO @ Tue, 30 Jun 2020 02:07:08: #1 tags after filtering in treatment: 20806275 INFO @ Tue, 30 Jun 2020 02:07:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:07:08: #1 finished! INFO @ Tue, 30 Jun 2020 02:07:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:07:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:07:09: #2 number of paired peaks: 118 WARNING @ Tue, 30 Jun 2020 02:07:09: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 30 Jun 2020 02:07:09: start model_add_line... INFO @ Tue, 30 Jun 2020 02:07:09: start X-correlation... INFO @ Tue, 30 Jun 2020 02:07:09: end of X-cor INFO @ Tue, 30 Jun 2020 02:07:09: #2 finished! INFO @ Tue, 30 Jun 2020 02:07:09: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:07:09: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 30 Jun 2020 02:07:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.05_model.r WARNING @ Tue, 30 Jun 2020 02:07:09: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:07:09: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 30 Jun 2020 02:07:09: #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 02:07:09: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:07:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:07:11: 9000000 INFO @ Tue, 30 Jun 2020 02:07:13: 16000000 INFO @ Tue, 30 Jun 2020 02:07:17: 10000000 INFO @ Tue, 30 Jun 2020 02:07:19: 17000000 INFO @ Tue, 30 Jun 2020 02:07:23: 11000000 INFO @ Tue, 30 Jun 2020 02:07:25: 18000000 INFO @ Tue, 30 Jun 2020 02:07:30: 12000000 INFO @ Tue, 30 Jun 2020 02:07:31: 19000000 INFO @ Tue, 30 Jun 2020 02:07:36: 13000000 INFO @ Tue, 30 Jun 2020 02:07:36: 20000000 INFO @ Tue, 30 Jun 2020 02:07:41: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:07:41: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:07:41: #1 total tags in treatment: 20806275 INFO @ Tue, 30 Jun 2020 02:07:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:07:41: #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 02:07:42: #1 tags after filtering in treatment: 20806275 INFO @ Tue, 30 Jun 2020 02:07:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:07:42: #1 finished! INFO @ Tue, 30 Jun 2020 02:07:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:07:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:07:43: 14000000 INFO @ Tue, 30 Jun 2020 02:07:43: #2 number of paired peaks: 118 WARNING @ Tue, 30 Jun 2020 02:07:43: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 30 Jun 2020 02:07:43: start model_add_line... INFO @ Tue, 30 Jun 2020 02:07:43: start X-correlation... INFO @ Tue, 30 Jun 2020 02:07:43: end of X-cor INFO @ Tue, 30 Jun 2020 02:07:43: #2 finished! INFO @ Tue, 30 Jun 2020 02:07:43: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:07:43: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 30 Jun 2020 02:07:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.10_model.r WARNING @ Tue, 30 Jun 2020 02:07:43: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:07:43: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 30 Jun 2020 02:07:43: #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 02:07:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:07:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:07:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:07:49: 15000000 INFO @ Tue, 30 Jun 2020 02:07:55: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:08:01: 17000000 INFO @ Tue, 30 Jun 2020 02:08:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:08:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:08:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.05_summits.bed INFO @ Tue, 30 Jun 2020 02:08:04: Done! pass1 - making usageList (634 chroms): 1 millis pass2 - checking and writing primary data (2675 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:08:07: 18000000 INFO @ Tue, 30 Jun 2020 02:08:13: 19000000 INFO @ Tue, 30 Jun 2020 02:08:20: 20000000 INFO @ Tue, 30 Jun 2020 02:08:20: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:08:25: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:08:25: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:08:25: #1 total tags in treatment: 20806275 INFO @ Tue, 30 Jun 2020 02:08:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:08:25: #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 02:08:26: #1 tags after filtering in treatment: 20806275 INFO @ Tue, 30 Jun 2020 02:08:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:08:26: #1 finished! INFO @ Tue, 30 Jun 2020 02:08:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:08:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:08:27: #2 number of paired peaks: 118 WARNING @ Tue, 30 Jun 2020 02:08:27: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 30 Jun 2020 02:08:27: start model_add_line... INFO @ Tue, 30 Jun 2020 02:08:27: start X-correlation... INFO @ Tue, 30 Jun 2020 02:08:27: end of X-cor INFO @ Tue, 30 Jun 2020 02:08:27: #2 finished! INFO @ Tue, 30 Jun 2020 02:08:27: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:08:27: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 30 Jun 2020 02:08:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.20_model.r WARNING @ Tue, 30 Jun 2020 02:08:27: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:08:27: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 30 Jun 2020 02:08:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:08:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:08:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:08:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:08:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:08:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.10_summits.bed INFO @ Tue, 30 Jun 2020 02:08:38: Done! pass1 - making usageList (461 chroms): 1 millis pass2 - checking and writing primary data (1258 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:09:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:09:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:09:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:09:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1847050/SRX1847050.20_summits.bed INFO @ Tue, 30 Jun 2020 02:09:20: Done! pass1 - making usageList (102 chroms): 1 millis pass2 - checking and writing primary data (207 records, 4 fields): 3 millis CompletedMACS2peakCalling