Job ID = 6529238 SRX = SRX1084161 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: 00:05:18 21974733 reads; of these: 21974733 (100.00%) were unpaired; of these: 2516258 (11.45%) aligned 0 times 15949270 (72.58%) aligned exactly 1 time 3509205 (15.97%) aligned >1 times 88.55% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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] 3259577 / 19458475 = 0.1675 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 01:49:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.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 01:49:18: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:49:18: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:49:23: 1000000 INFO @ Tue, 30 Jun 2020 01:49:27: 2000000 INFO @ Tue, 30 Jun 2020 01:49:32: 3000000 INFO @ Tue, 30 Jun 2020 01:49:36: 4000000 INFO @ Tue, 30 Jun 2020 01:49:41: 5000000 INFO @ Tue, 30 Jun 2020 01:49:45: 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 01:49:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.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 01:49:48: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:49:48: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:49:50: 7000000 INFO @ Tue, 30 Jun 2020 01:49:53: 1000000 INFO @ Tue, 30 Jun 2020 01:49:55: 8000000 INFO @ Tue, 30 Jun 2020 01:49:57: 2000000 INFO @ Tue, 30 Jun 2020 01:49:59: 9000000 INFO @ Tue, 30 Jun 2020 01:50:02: 3000000 INFO @ Tue, 30 Jun 2020 01:50:04: 10000000 INFO @ Tue, 30 Jun 2020 01:50:06: 4000000 INFO @ Tue, 30 Jun 2020 01:50:08: 11000000 INFO @ Tue, 30 Jun 2020 01:50:11: 5000000 INFO @ Tue, 30 Jun 2020 01:50:13: 12000000 INFO @ Tue, 30 Jun 2020 01:50:16: 6000000 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 01:50:18: 13000000 INFO @ Tue, 30 Jun 2020 01:50:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.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 01:50:18: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:50:18: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:50:20: 7000000 INFO @ Tue, 30 Jun 2020 01:50:22: 14000000 INFO @ Tue, 30 Jun 2020 01:50:23: 1000000 INFO @ Tue, 30 Jun 2020 01:50:25: 8000000 INFO @ Tue, 30 Jun 2020 01:50:27: 15000000 INFO @ Tue, 30 Jun 2020 01:50:27: 2000000 INFO @ Tue, 30 Jun 2020 01:50:29: 9000000 INFO @ Tue, 30 Jun 2020 01:50:32: 16000000 INFO @ Tue, 30 Jun 2020 01:50:32: 3000000 INFO @ Tue, 30 Jun 2020 01:50:33: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 01:50:33: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 01:50:33: #1 total tags in treatment: 16198898 INFO @ Tue, 30 Jun 2020 01:50:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:50:33: #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 01:50:33: #1 tags after filtering in treatment: 16198829 INFO @ Tue, 30 Jun 2020 01:50:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:50:33: #1 finished! INFO @ Tue, 30 Jun 2020 01:50:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:50:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:50:34: 10000000 INFO @ Tue, 30 Jun 2020 01:50:34: #2 number of paired peaks: 233 WARNING @ Tue, 30 Jun 2020 01:50:34: Fewer paired peaks (233) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 233 pairs to build model! INFO @ Tue, 30 Jun 2020 01:50:34: start model_add_line... INFO @ Tue, 30 Jun 2020 01:50:34: start X-correlation... INFO @ Tue, 30 Jun 2020 01:50:34: end of X-cor INFO @ Tue, 30 Jun 2020 01:50:34: #2 finished! INFO @ Tue, 30 Jun 2020 01:50:34: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 01:50:34: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 30 Jun 2020 01:50:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.05_model.r WARNING @ Tue, 30 Jun 2020 01:50:34: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:50:34: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 30 Jun 2020 01:50:34: #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 01:50:34: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:50:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:50:37: 4000000 INFO @ Tue, 30 Jun 2020 01:50:38: 11000000 INFO @ Tue, 30 Jun 2020 01:50:41: 5000000 INFO @ Tue, 30 Jun 2020 01:50:43: 12000000 INFO @ Tue, 30 Jun 2020 01:50:46: 6000000 INFO @ Tue, 30 Jun 2020 01:50:48: 13000000 INFO @ Tue, 30 Jun 2020 01:50:50: 7000000 INFO @ Tue, 30 Jun 2020 01:50:52: 14000000 INFO @ Tue, 30 Jun 2020 01:50:55: 8000000 INFO @ Tue, 30 Jun 2020 01:50:57: 15000000 INFO @ Tue, 30 Jun 2020 01:51:00: 9000000 INFO @ Tue, 30 Jun 2020 01:51:02: 16000000 INFO @ Tue, 30 Jun 2020 01:51:03: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 01:51:03: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 01:51:03: #1 total tags in treatment: 16198898 INFO @ Tue, 30 Jun 2020 01:51:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:51:03: #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 01:51:03: #1 tags after filtering in treatment: 16198829 INFO @ Tue, 30 Jun 2020 01:51:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:51:03: #1 finished! INFO @ Tue, 30 Jun 2020 01:51:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:51:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:51:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:51:04: 10000000 INFO @ Tue, 30 Jun 2020 01:51:04: #2 number of paired peaks: 233 WARNING @ Tue, 30 Jun 2020 01:51:04: Fewer paired peaks (233) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 233 pairs to build model! INFO @ Tue, 30 Jun 2020 01:51:04: start model_add_line... INFO @ Tue, 30 Jun 2020 01:51:04: start X-correlation... INFO @ Tue, 30 Jun 2020 01:51:04: end of X-cor INFO @ Tue, 30 Jun 2020 01:51:04: #2 finished! INFO @ Tue, 30 Jun 2020 01:51:04: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 01:51:04: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 30 Jun 2020 01:51:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.10_model.r WARNING @ Tue, 30 Jun 2020 01:51:04: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:51:04: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 30 Jun 2020 01:51:04: #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 01:51:04: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:51:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:51:09: 11000000 INFO @ Tue, 30 Jun 2020 01:51:13: 12000000 INFO @ Tue, 30 Jun 2020 01:51:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:51:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:51:18: 13000000 INFO @ Tue, 30 Jun 2020 01:51:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.05_summits.bed INFO @ Tue, 30 Jun 2020 01:51:18: Done! pass1 - making usageList (565 chroms): 1 millis pass2 - checking and writing primary data (4931 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:51:23: 14000000 INFO @ Tue, 30 Jun 2020 01:51:27: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:51:32: 16000000 INFO @ Tue, 30 Jun 2020 01:51:33: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 01:51:33: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 01:51:33: #1 total tags in treatment: 16198898 INFO @ Tue, 30 Jun 2020 01:51:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:51:33: #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 01:51:34: #1 tags after filtering in treatment: 16198829 INFO @ Tue, 30 Jun 2020 01:51:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:51:34: #1 finished! INFO @ Tue, 30 Jun 2020 01:51:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:51:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:51:34: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:51:35: #2 number of paired peaks: 233 WARNING @ Tue, 30 Jun 2020 01:51:35: Fewer paired peaks (233) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 233 pairs to build model! INFO @ Tue, 30 Jun 2020 01:51:35: start model_add_line... INFO @ Tue, 30 Jun 2020 01:51:35: start X-correlation... INFO @ Tue, 30 Jun 2020 01:51:35: end of X-cor INFO @ Tue, 30 Jun 2020 01:51:35: #2 finished! INFO @ Tue, 30 Jun 2020 01:51:35: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 01:51:35: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 30 Jun 2020 01:51:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.20_model.r WARNING @ Tue, 30 Jun 2020 01:51:35: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:51:35: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 30 Jun 2020 01:51:35: #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 01:51:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:51:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:51:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:51:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:51:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.10_summits.bed INFO @ Tue, 30 Jun 2020 01:51:48: Done! pass1 - making usageList (475 chroms): 1 millis pass2 - checking and writing primary data (2170 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:52:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:52:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:52:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:52:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1084161/SRX1084161.20_summits.bed INFO @ Tue, 30 Jun 2020 01:52:19: Done! pass1 - making usageList (207 chroms): 1 millis pass2 - checking and writing primary data (452 records, 4 fields): 8 millis CompletedMACS2peakCalling