Job ID = 6529351 SRX = SRX2011089 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: 00:07:56 15829804 reads; of these: 15829804 (100.00%) were unpaired; of these: 628467 (3.97%) aligned 0 times 12299500 (77.70%) aligned exactly 1 time 2901837 (18.33%) aligned >1 times 96.03% overall alignment rate Time searching: 00:07:56 Overall time: 00:07:56 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] 1032074 / 15201337 = 0.0679 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 02:23:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.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 02:23:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:23:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:24:09: 1000000 INFO @ Tue, 30 Jun 2020 02:24:19: 2000000 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 02:24:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.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 02:24:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:24:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:24:29: 3000000 INFO @ Tue, 30 Jun 2020 02:24:39: 4000000 INFO @ Tue, 30 Jun 2020 02:24:39: 1000000 INFO @ Tue, 30 Jun 2020 02:24:49: 5000000 INFO @ Tue, 30 Jun 2020 02:24:49: 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 02:24:59: 6000000 INFO @ Tue, 30 Jun 2020 02:24:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.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 02:24:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:24:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:24:59: 3000000 INFO @ Tue, 30 Jun 2020 02:25:09: 7000000 INFO @ Tue, 30 Jun 2020 02:25:09: 1000000 INFO @ Tue, 30 Jun 2020 02:25:09: 4000000 INFO @ Tue, 30 Jun 2020 02:25:19: 8000000 INFO @ Tue, 30 Jun 2020 02:25:20: 2000000 INFO @ Tue, 30 Jun 2020 02:25:20: 5000000 INFO @ Tue, 30 Jun 2020 02:25:30: 9000000 INFO @ Tue, 30 Jun 2020 02:25:30: 3000000 INFO @ Tue, 30 Jun 2020 02:25:30: 6000000 INFO @ Tue, 30 Jun 2020 02:25:40: 10000000 INFO @ Tue, 30 Jun 2020 02:25:40: 4000000 INFO @ Tue, 30 Jun 2020 02:25:40: 7000000 INFO @ Tue, 30 Jun 2020 02:25:50: 11000000 INFO @ Tue, 30 Jun 2020 02:25:51: 8000000 INFO @ Tue, 30 Jun 2020 02:25:51: 5000000 INFO @ Tue, 30 Jun 2020 02:26:00: 9000000 INFO @ Tue, 30 Jun 2020 02:26:00: 12000000 INFO @ Tue, 30 Jun 2020 02:26:01: 6000000 INFO @ Tue, 30 Jun 2020 02:26:10: 13000000 INFO @ Tue, 30 Jun 2020 02:26:11: 7000000 INFO @ Tue, 30 Jun 2020 02:26:11: 10000000 INFO @ Tue, 30 Jun 2020 02:26:21: 8000000 INFO @ Tue, 30 Jun 2020 02:26:21: 14000000 INFO @ Tue, 30 Jun 2020 02:26:21: 11000000 INFO @ Tue, 30 Jun 2020 02:26:23: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:26:23: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:26:23: #1 total tags in treatment: 14169263 INFO @ Tue, 30 Jun 2020 02:26:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:26:23: #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 02:26:23: #1 tags after filtering in treatment: 14169226 INFO @ Tue, 30 Jun 2020 02:26:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:26:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:26:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:26:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:26:24: #2 number of paired peaks: 190 WARNING @ Tue, 30 Jun 2020 02:26:24: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Tue, 30 Jun 2020 02:26:24: start model_add_line... INFO @ Tue, 30 Jun 2020 02:26:24: start X-correlation... INFO @ Tue, 30 Jun 2020 02:26:24: end of X-cor INFO @ Tue, 30 Jun 2020 02:26:24: #2 finished! INFO @ Tue, 30 Jun 2020 02:26:24: #2 predicted fragment length is 97 bps INFO @ Tue, 30 Jun 2020 02:26:24: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 30 Jun 2020 02:26:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.05_model.r WARNING @ Tue, 30 Jun 2020 02:26:24: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:26:24: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Tue, 30 Jun 2020 02:26:24: #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 02:26:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:26:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:26:30: 9000000 INFO @ Tue, 30 Jun 2020 02:26:32: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:26:40: 10000000 INFO @ Tue, 30 Jun 2020 02:26:41: 13000000 INFO @ Tue, 30 Jun 2020 02:26:49: 11000000 INFO @ Tue, 30 Jun 2020 02:26:50: 14000000 INFO @ Tue, 30 Jun 2020 02:26:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:26:52: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:26:52: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:26:52: #1 total tags in treatment: 14169263 INFO @ Tue, 30 Jun 2020 02:26:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:26:52: #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 02:26:53: #1 tags after filtering in treatment: 14169226 INFO @ Tue, 30 Jun 2020 02:26:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:26:53: #1 finished! INFO @ Tue, 30 Jun 2020 02:26:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:26:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:26:54: #2 number of paired peaks: 190 WARNING @ Tue, 30 Jun 2020 02:26:54: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Tue, 30 Jun 2020 02:26:54: start model_add_line... INFO @ Tue, 30 Jun 2020 02:26:54: start X-correlation... INFO @ Tue, 30 Jun 2020 02:26:54: end of X-cor INFO @ Tue, 30 Jun 2020 02:26:54: #2 finished! INFO @ Tue, 30 Jun 2020 02:26:54: #2 predicted fragment length is 97 bps INFO @ Tue, 30 Jun 2020 02:26:54: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 30 Jun 2020 02:26:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.10_model.r WARNING @ Tue, 30 Jun 2020 02:26:54: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:26:54: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Tue, 30 Jun 2020 02:26:54: #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 02:26:54: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:26:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:26:58: 12000000 INFO @ Tue, 30 Jun 2020 02:27:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:27:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:27:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.05_summits.bed INFO @ Tue, 30 Jun 2020 02:27:04: Done! pass1 - making usageList (497 chroms): 2 millis pass2 - checking and writing primary data (1304 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:27:07: 13000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:27:16: 14000000 INFO @ Tue, 30 Jun 2020 02:27:18: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:27:18: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:27:18: #1 total tags in treatment: 14169263 INFO @ Tue, 30 Jun 2020 02:27:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:27:18: #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 02:27:19: #1 tags after filtering in treatment: 14169226 INFO @ Tue, 30 Jun 2020 02:27:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:27:19: #1 finished! INFO @ Tue, 30 Jun 2020 02:27:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:27:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:27:20: #2 number of paired peaks: 190 WARNING @ Tue, 30 Jun 2020 02:27:20: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Tue, 30 Jun 2020 02:27:20: start model_add_line... INFO @ Tue, 30 Jun 2020 02:27:20: start X-correlation... INFO @ Tue, 30 Jun 2020 02:27:20: end of X-cor INFO @ Tue, 30 Jun 2020 02:27:20: #2 finished! INFO @ Tue, 30 Jun 2020 02:27:20: #2 predicted fragment length is 97 bps INFO @ Tue, 30 Jun 2020 02:27:20: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 30 Jun 2020 02:27:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.20_model.r WARNING @ Tue, 30 Jun 2020 02:27:20: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:27:20: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Tue, 30 Jun 2020 02:27:20: #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 02:27:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:27:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:27:20: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:27:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:27:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:27:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.10_summits.bed INFO @ Tue, 30 Jun 2020 02:27:33: Done! pass1 - making usageList (361 chroms): 1 millis pass2 - checking and writing primary data (729 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:27:45: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:27:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:27:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:27:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2011089/SRX2011089.20_summits.bed INFO @ Tue, 30 Jun 2020 02:27:59: Done! pass1 - making usageList (177 chroms): 1 millis pass2 - checking and writing primary data (309 records, 4 fields): 10 millis CompletedMACS2peakCalling