Job ID = 6529501 SRX = SRX287849 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: 00:06:07 21823290 reads; of these: 21823290 (100.00%) were unpaired; of these: 1412797 (6.47%) aligned 0 times 15655266 (71.74%) aligned exactly 1 time 4755227 (21.79%) aligned >1 times 93.53% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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 12 files... [bam_rmdupse_core] 2760282 / 20410493 = 0.1352 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 02:15:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.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 02:15:48: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:15:48: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:15:55: 1000000 INFO @ Tue, 30 Jun 2020 02:16:02: 2000000 INFO @ Tue, 30 Jun 2020 02:16:08: 3000000 INFO @ Tue, 30 Jun 2020 02:16:15: 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, 30 Jun 2020 02:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.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 02:16:18: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:16:18: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:16:22: 5000000 INFO @ Tue, 30 Jun 2020 02:16:26: 1000000 INFO @ Tue, 30 Jun 2020 02:16:29: 6000000 INFO @ Tue, 30 Jun 2020 02:16:33: 2000000 INFO @ Tue, 30 Jun 2020 02:16:36: 7000000 INFO @ Tue, 30 Jun 2020 02:16:39: 3000000 INFO @ Tue, 30 Jun 2020 02:16:43: 8000000 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 02:16:46: 4000000 INFO @ Tue, 30 Jun 2020 02:16:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.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 02:16:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:16:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:16:49: 9000000 INFO @ Tue, 30 Jun 2020 02:16:53: 5000000 INFO @ Tue, 30 Jun 2020 02:16:56: 1000000 INFO @ Tue, 30 Jun 2020 02:16:56: 10000000 INFO @ Tue, 30 Jun 2020 02:17:00: 6000000 INFO @ Tue, 30 Jun 2020 02:17:03: 2000000 INFO @ Tue, 30 Jun 2020 02:17:03: 11000000 INFO @ Tue, 30 Jun 2020 02:17:07: 7000000 INFO @ Tue, 30 Jun 2020 02:17:09: 3000000 INFO @ Tue, 30 Jun 2020 02:17:10: 12000000 INFO @ Tue, 30 Jun 2020 02:17:14: 8000000 INFO @ Tue, 30 Jun 2020 02:17:16: 4000000 INFO @ Tue, 30 Jun 2020 02:17:17: 13000000 INFO @ Tue, 30 Jun 2020 02:17:21: 9000000 INFO @ Tue, 30 Jun 2020 02:17:23: 5000000 INFO @ Tue, 30 Jun 2020 02:17:25: 14000000 INFO @ Tue, 30 Jun 2020 02:17:28: 10000000 INFO @ Tue, 30 Jun 2020 02:17:30: 6000000 INFO @ Tue, 30 Jun 2020 02:17:32: 15000000 INFO @ Tue, 30 Jun 2020 02:17:35: 11000000 INFO @ Tue, 30 Jun 2020 02:17:37: 7000000 INFO @ Tue, 30 Jun 2020 02:17:39: 16000000 INFO @ Tue, 30 Jun 2020 02:17:42: 12000000 INFO @ Tue, 30 Jun 2020 02:17:44: 8000000 INFO @ Tue, 30 Jun 2020 02:17:46: 17000000 INFO @ Tue, 30 Jun 2020 02:17:49: 13000000 INFO @ Tue, 30 Jun 2020 02:17:50: 9000000 INFO @ Tue, 30 Jun 2020 02:17:51: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:17:51: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:17:51: #1 total tags in treatment: 17650211 INFO @ Tue, 30 Jun 2020 02:17:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:17:51: #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 02:17:52: #1 tags after filtering in treatment: 17650208 INFO @ Tue, 30 Jun 2020 02:17:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:17:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:17:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:17:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:17:53: #2 number of paired peaks: 349 WARNING @ Tue, 30 Jun 2020 02:17:53: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Tue, 30 Jun 2020 02:17:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:17:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:17:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:17:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:17:53: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 02:17:53: #2 alternative fragment length(s) may be 2,36 bps INFO @ Tue, 30 Jun 2020 02:17:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.05_model.r WARNING @ Tue, 30 Jun 2020 02:17:53: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:17:53: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Tue, 30 Jun 2020 02:17:53: #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 02:17:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:17:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:17:56: 14000000 INFO @ Tue, 30 Jun 2020 02:17:57: 10000000 INFO @ Tue, 30 Jun 2020 02:18:04: 11000000 INFO @ Tue, 30 Jun 2020 02:18:04: 15000000 INFO @ Tue, 30 Jun 2020 02:18:10: 12000000 INFO @ Tue, 30 Jun 2020 02:18:11: 16000000 INFO @ Tue, 30 Jun 2020 02:18:18: 13000000 INFO @ Tue, 30 Jun 2020 02:18:18: 17000000 INFO @ Tue, 30 Jun 2020 02:18:23: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:18:23: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:18:23: #1 total tags in treatment: 17650211 INFO @ Tue, 30 Jun 2020 02:18:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:18:23: #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 02:18:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:18:24: #1 tags after filtering in treatment: 17650208 INFO @ Tue, 30 Jun 2020 02:18:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:18:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:18:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:18:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:18:25: #2 number of paired peaks: 349 WARNING @ Tue, 30 Jun 2020 02:18:25: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Tue, 30 Jun 2020 02:18:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:18:25: 14000000 INFO @ Tue, 30 Jun 2020 02:18:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:18:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:18:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:18:25: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 02:18:25: #2 alternative fragment length(s) may be 2,36 bps INFO @ Tue, 30 Jun 2020 02:18:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.10_model.r WARNING @ Tue, 30 Jun 2020 02:18:25: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:18:25: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Tue, 30 Jun 2020 02:18:25: #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 02:18:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:18:25: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:18:32: 15000000 INFO @ Tue, 30 Jun 2020 02:18:39: 16000000 INFO @ Tue, 30 Jun 2020 02:18:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:18:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:18:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.05_summits.bed INFO @ Tue, 30 Jun 2020 02:18:40: Done! pass1 - making usageList (532 chroms): 2 millis pass2 - checking and writing primary data (2253 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:18:46: 17000000 INFO @ Tue, 30 Jun 2020 02:18:51: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:18:51: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:18:51: #1 total tags in treatment: 17650211 INFO @ Tue, 30 Jun 2020 02:18:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:18:51: #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 02:18:52: #1 tags after filtering in treatment: 17650208 INFO @ Tue, 30 Jun 2020 02:18:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:18:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:18:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:18:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:18:53: #2 number of paired peaks: 349 WARNING @ Tue, 30 Jun 2020 02:18:53: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Tue, 30 Jun 2020 02:18:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:18:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:18:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:18:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:18:53: #2 predicted fragment length is 36 bps INFO @ Tue, 30 Jun 2020 02:18:53: #2 alternative fragment length(s) may be 2,36 bps INFO @ Tue, 30 Jun 2020 02:18:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.20_model.r WARNING @ Tue, 30 Jun 2020 02:18:53: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:18:53: #2 You may need to consider one of the other alternative d(s): 2,36 WARNING @ Tue, 30 Jun 2020 02:18:53: #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 02:18:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:18:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:18:55: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:19:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:19:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:19:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.10_summits.bed INFO @ Tue, 30 Jun 2020 02:19:11: Done! pass1 - making usageList (461 chroms): 2 millis pass2 - checking and writing primary data (1778 records, 4 fields): 27 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:19:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:19:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:19:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:19:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287849/SRX287849.20_summits.bed INFO @ Tue, 30 Jun 2020 02:19:39: Done! pass1 - making usageList (260 chroms): 1 millis pass2 - checking and writing primary data (535 records, 4 fields): 16 millis CompletedMACS2peakCalling