Job ID = 6529521 SRX = SRX287905 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: 00:05:04 18412477 reads; of these: 18412477 (100.00%) were unpaired; of these: 1075244 (5.84%) aligned 0 times 13617929 (73.96%) aligned exactly 1 time 3719304 (20.20%) aligned >1 times 94.16% overall alignment rate Time searching: 00:05:04 Overall time: 00:05:04 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] 1587598 / 17337233 = 0.0916 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 02:30:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.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 02:30:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:30:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:30:16: 1000000 INFO @ Tue, 30 Jun 2020 02:30:24: 2000000 INFO @ Tue, 30 Jun 2020 02:30:31: 3000000 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 02:30:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.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 02:30:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:30:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:30:38: 4000000 INFO @ Tue, 30 Jun 2020 02:30:46: 1000000 INFO @ Tue, 30 Jun 2020 02:30:46: 5000000 INFO @ Tue, 30 Jun 2020 02:30:53: 2000000 INFO @ Tue, 30 Jun 2020 02:30:54: 6000000 INFO @ Tue, 30 Jun 2020 02:31:01: 3000000 INFO @ Tue, 30 Jun 2020 02:31:02: 7000000 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 02:31:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.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 02:31:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:31:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:31:08: 4000000 INFO @ Tue, 30 Jun 2020 02:31:10: 8000000 INFO @ Tue, 30 Jun 2020 02:31:16: 1000000 INFO @ Tue, 30 Jun 2020 02:31:16: 5000000 INFO @ Tue, 30 Jun 2020 02:31:18: 9000000 INFO @ Tue, 30 Jun 2020 02:31:24: 2000000 INFO @ Tue, 30 Jun 2020 02:31:24: 6000000 INFO @ Tue, 30 Jun 2020 02:31:26: 10000000 INFO @ Tue, 30 Jun 2020 02:31:31: 3000000 INFO @ Tue, 30 Jun 2020 02:31:32: 7000000 INFO @ Tue, 30 Jun 2020 02:31:34: 11000000 INFO @ Tue, 30 Jun 2020 02:31:39: 4000000 INFO @ Tue, 30 Jun 2020 02:31:39: 8000000 INFO @ Tue, 30 Jun 2020 02:31:42: 12000000 INFO @ Tue, 30 Jun 2020 02:31:47: 5000000 INFO @ Tue, 30 Jun 2020 02:31:47: 9000000 INFO @ Tue, 30 Jun 2020 02:31:51: 13000000 INFO @ Tue, 30 Jun 2020 02:31:54: 6000000 INFO @ Tue, 30 Jun 2020 02:31:55: 10000000 INFO @ Tue, 30 Jun 2020 02:31:59: 14000000 INFO @ Tue, 30 Jun 2020 02:32:02: 7000000 INFO @ Tue, 30 Jun 2020 02:32:03: 11000000 INFO @ Tue, 30 Jun 2020 02:32:08: 15000000 INFO @ Tue, 30 Jun 2020 02:32:10: 8000000 INFO @ Tue, 30 Jun 2020 02:32:11: 12000000 INFO @ Tue, 30 Jun 2020 02:32:14: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:32:14: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:32:14: #1 total tags in treatment: 15749635 INFO @ Tue, 30 Jun 2020 02:32:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:32:14: #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 02:32:15: #1 tags after filtering in treatment: 15749635 INFO @ Tue, 30 Jun 2020 02:32:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:32:15: #1 finished! INFO @ Tue, 30 Jun 2020 02:32:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:32:16: #2 number of paired peaks: 231 WARNING @ Tue, 30 Jun 2020 02:32:16: Fewer paired peaks (231) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 231 pairs to build model! INFO @ Tue, 30 Jun 2020 02:32:16: start model_add_line... INFO @ Tue, 30 Jun 2020 02:32:16: start X-correlation... INFO @ Tue, 30 Jun 2020 02:32:16: end of X-cor INFO @ Tue, 30 Jun 2020 02:32:16: #2 finished! INFO @ Tue, 30 Jun 2020 02:32:16: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:32:16: #2 alternative fragment length(s) may be 4,45 bps INFO @ Tue, 30 Jun 2020 02:32:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.05_model.r WARNING @ Tue, 30 Jun 2020 02:32:16: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:32:16: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Tue, 30 Jun 2020 02:32:16: #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 02:32:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:32:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:32:17: 9000000 INFO @ Tue, 30 Jun 2020 02:32:19: 13000000 INFO @ Tue, 30 Jun 2020 02:32:25: 10000000 INFO @ Tue, 30 Jun 2020 02:32:26: 14000000 INFO @ Tue, 30 Jun 2020 02:32:32: 11000000 INFO @ Tue, 30 Jun 2020 02:32:34: 15000000 INFO @ Tue, 30 Jun 2020 02:32:39: 12000000 INFO @ Tue, 30 Jun 2020 02:32:39: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:32:39: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:32:39: #1 total tags in treatment: 15749635 INFO @ Tue, 30 Jun 2020 02:32:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:32:39: #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 02:32:40: #1 tags after filtering in treatment: 15749635 INFO @ Tue, 30 Jun 2020 02:32:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:32:40: #1 finished! INFO @ Tue, 30 Jun 2020 02:32:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:32:41: #2 number of paired peaks: 231 WARNING @ Tue, 30 Jun 2020 02:32:41: Fewer paired peaks (231) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 231 pairs to build model! INFO @ Tue, 30 Jun 2020 02:32:41: start model_add_line... INFO @ Tue, 30 Jun 2020 02:32:41: start X-correlation... INFO @ Tue, 30 Jun 2020 02:32:41: end of X-cor INFO @ Tue, 30 Jun 2020 02:32:41: #2 finished! INFO @ Tue, 30 Jun 2020 02:32:41: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:32:41: #2 alternative fragment length(s) may be 4,45 bps INFO @ Tue, 30 Jun 2020 02:32:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.10_model.r WARNING @ Tue, 30 Jun 2020 02:32:41: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:32:41: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Tue, 30 Jun 2020 02:32:41: #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 02:32:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:32:41: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:32:46: 13000000 INFO @ Tue, 30 Jun 2020 02:32:48: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:32:52: 14000000 INFO @ Tue, 30 Jun 2020 02:32:59: 15000000 INFO @ Tue, 30 Jun 2020 02:33:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:33:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:33:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.05_summits.bed INFO @ Tue, 30 Jun 2020 02:33:03: Done! INFO @ Tue, 30 Jun 2020 02:33:04: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:33:04: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:33:04: #1 total tags in treatment: 15749635 INFO @ Tue, 30 Jun 2020 02:33:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:33:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (511 chroms): 2 millis pass2 - checking and writing primary data (2081 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:33:04: #1 tags after filtering in treatment: 15749635 INFO @ Tue, 30 Jun 2020 02:33:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:33:04: #1 finished! INFO @ Tue, 30 Jun 2020 02:33:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:33:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:33:05: #2 number of paired peaks: 231 WARNING @ Tue, 30 Jun 2020 02:33:05: Fewer paired peaks (231) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 231 pairs to build model! INFO @ Tue, 30 Jun 2020 02:33:05: start model_add_line... INFO @ Tue, 30 Jun 2020 02:33:05: start X-correlation... INFO @ Tue, 30 Jun 2020 02:33:05: end of X-cor INFO @ Tue, 30 Jun 2020 02:33:05: #2 finished! INFO @ Tue, 30 Jun 2020 02:33:05: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:33:05: #2 alternative fragment length(s) may be 4,45 bps INFO @ Tue, 30 Jun 2020 02:33:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.20_model.r WARNING @ Tue, 30 Jun 2020 02:33:05: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:33:05: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Tue, 30 Jun 2020 02:33:05: #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 02:33:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:33:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:33:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:33:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:33:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:33:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.10_summits.bed INFO @ Tue, 30 Jun 2020 02:33:30: Done! pass1 - making usageList (421 chroms): 2 millis pass2 - checking and writing primary data (1355 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:33:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:33:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:33:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:33:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287905/SRX287905.20_summits.bed INFO @ Tue, 30 Jun 2020 02:33:55: Done! pass1 - making usageList (205 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 8 millis CompletedMACS2peakCalling