Job ID = 6529465 SRX = SRX287677 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: 00:04:59 18412477 reads; of these: 18412477 (100.00%) were unpaired; of these: 1075220 (5.84%) aligned 0 times 13617941 (73.96%) aligned exactly 1 time 3719316 (20.20%) aligned >1 times 94.16% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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] 1587740 / 17337257 = 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 02:22:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.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 02:22:41: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:22:41: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:22:49: 1000000 INFO @ Tue, 30 Jun 2020 02:22:58: 2000000 INFO @ Tue, 30 Jun 2020 02:23:06: 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 02:23:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.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 02:23:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:23:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:23:14: 4000000 INFO @ Tue, 30 Jun 2020 02:23:21: 1000000 INFO @ Tue, 30 Jun 2020 02:23:22: 5000000 INFO @ Tue, 30 Jun 2020 02:23:31: 6000000 INFO @ Tue, 30 Jun 2020 02:23:31: 2000000 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 02:23:39: 7000000 INFO @ Tue, 30 Jun 2020 02:23:41: 3000000 INFO @ Tue, 30 Jun 2020 02:23:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.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 02:23:41: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:23:41: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:23:48: 8000000 INFO @ Tue, 30 Jun 2020 02:23:50: 1000000 INFO @ Tue, 30 Jun 2020 02:23:51: 4000000 INFO @ Tue, 30 Jun 2020 02:23:56: 9000000 INFO @ Tue, 30 Jun 2020 02:23:59: 2000000 INFO @ Tue, 30 Jun 2020 02:24:00: 5000000 INFO @ Tue, 30 Jun 2020 02:24:05: 10000000 INFO @ Tue, 30 Jun 2020 02:24:07: 3000000 INFO @ Tue, 30 Jun 2020 02:24:09: 6000000 INFO @ Tue, 30 Jun 2020 02:24:14: 11000000 INFO @ Tue, 30 Jun 2020 02:24:16: 4000000 INFO @ Tue, 30 Jun 2020 02:24:18: 7000000 INFO @ Tue, 30 Jun 2020 02:24:23: 12000000 INFO @ Tue, 30 Jun 2020 02:24:25: 5000000 INFO @ Tue, 30 Jun 2020 02:24:27: 8000000 INFO @ Tue, 30 Jun 2020 02:24:32: 13000000 INFO @ Tue, 30 Jun 2020 02:24:33: 6000000 INFO @ Tue, 30 Jun 2020 02:24:36: 9000000 INFO @ Tue, 30 Jun 2020 02:24:41: 14000000 INFO @ Tue, 30 Jun 2020 02:24:42: 7000000 INFO @ Tue, 30 Jun 2020 02:24:45: 10000000 INFO @ Tue, 30 Jun 2020 02:24:49: 15000000 INFO @ Tue, 30 Jun 2020 02:24:50: 8000000 INFO @ Tue, 30 Jun 2020 02:24:54: 11000000 INFO @ Tue, 30 Jun 2020 02:24:56: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:24:56: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:24:56: #1 total tags in treatment: 15749517 INFO @ Tue, 30 Jun 2020 02:24:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:56: #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 02:24:56: #1 tags after filtering in treatment: 15749516 INFO @ Tue, 30 Jun 2020 02:24:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:56: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:24:58: #2 number of paired peaks: 254 WARNING @ Tue, 30 Jun 2020 02:24:58: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 30 Jun 2020 02:24:58: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:58: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:58: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:58: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:58: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:24:58: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 02:24:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.05_model.r WARNING @ Tue, 30 Jun 2020 02:24:58: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:24:58: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 02:24:58: #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 02:24:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:58: 9000000 INFO @ Tue, 30 Jun 2020 02:25:03: 12000000 INFO @ Tue, 30 Jun 2020 02:25:06: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:25:13: 13000000 INFO @ Tue, 30 Jun 2020 02:25:14: 11000000 INFO @ Tue, 30 Jun 2020 02:25:21: 12000000 INFO @ Tue, 30 Jun 2020 02:25:23: 14000000 INFO @ Tue, 30 Jun 2020 02:25:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:25:29: 13000000 INFO @ Tue, 30 Jun 2020 02:25:31: 15000000 INFO @ Tue, 30 Jun 2020 02:25:37: 14000000 INFO @ Tue, 30 Jun 2020 02:25:38: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:25:38: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:25:38: #1 total tags in treatment: 15749517 INFO @ Tue, 30 Jun 2020 02:25:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:25:38: #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 02:25:39: #1 tags after filtering in treatment: 15749516 INFO @ Tue, 30 Jun 2020 02:25:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:25:39: #1 finished! INFO @ Tue, 30 Jun 2020 02:25:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:25:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:25:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:25:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:25:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.05_summits.bed INFO @ Tue, 30 Jun 2020 02:25:39: Done! pass1 - making usageList (506 chroms): 1 millis pass2 - checking and writing primary data (2070 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:25:40: #2 number of paired peaks: 254 WARNING @ Tue, 30 Jun 2020 02:25:40: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 30 Jun 2020 02:25:40: start model_add_line... INFO @ Tue, 30 Jun 2020 02:25:40: start X-correlation... INFO @ Tue, 30 Jun 2020 02:25:40: end of X-cor INFO @ Tue, 30 Jun 2020 02:25:40: #2 finished! INFO @ Tue, 30 Jun 2020 02:25:40: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:25:40: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 02:25:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.10_model.r WARNING @ Tue, 30 Jun 2020 02:25:40: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:25:40: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 02:25:40: #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 02:25:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:25:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:25:45: 15000000 INFO @ Tue, 30 Jun 2020 02:25:51: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:25:51: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:25:51: #1 total tags in treatment: 15749517 INFO @ Tue, 30 Jun 2020 02:25:51: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:25:51: #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 02:25:52: #1 tags after filtering in treatment: 15749516 INFO @ Tue, 30 Jun 2020 02:25:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:25:52: #1 finished! INFO @ Tue, 30 Jun 2020 02:25:52: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:25:53: #2 number of paired peaks: 254 WARNING @ Tue, 30 Jun 2020 02:25:53: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 30 Jun 2020 02:25:53: start model_add_line... INFO @ Tue, 30 Jun 2020 02:25:53: start X-correlation... INFO @ Tue, 30 Jun 2020 02:25:53: end of X-cor INFO @ Tue, 30 Jun 2020 02:25:53: #2 finished! INFO @ Tue, 30 Jun 2020 02:25:53: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:25:53: #2 alternative fragment length(s) may be 4,44 bps INFO @ Tue, 30 Jun 2020 02:25:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.20_model.r WARNING @ Tue, 30 Jun 2020 02:25:53: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:25:53: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Tue, 30 Jun 2020 02:25:53: #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 02:25:53: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:25:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:26:07: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:26:20: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:26:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:26:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:26:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.10_summits.bed INFO @ Tue, 30 Jun 2020 02:26:22: Done! pass1 - making usageList (419 chroms): 1 millis pass2 - checking and writing primary data (1338 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:26:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:26:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:26:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287677/SRX287677.20_summits.bed INFO @ Tue, 30 Jun 2020 02:26:34: Done! pass1 - making usageList (219 chroms): 1 millis pass2 - checking and writing primary data (443 records, 4 fields): 13 millis CompletedMACS2peakCalling