Job ID = 6529616 SRX = SRX3511945 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: 00:05:22 11385708 reads; of these: 11385708 (100.00%) were unpaired; of these: 2009248 (17.65%) aligned 0 times 7415827 (65.13%) aligned exactly 1 time 1960633 (17.22%) aligned >1 times 82.35% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 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_rmdupse_core] 565694 / 9376460 = 0.0603 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 02:36:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.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 02:36:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:36:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:36:28: 1000000 INFO @ Tue, 30 Jun 2020 02:36:35: 2000000 INFO @ Tue, 30 Jun 2020 02:36:43: 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 02:36:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.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 02:36:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:36:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:36:52: 4000000 INFO @ Tue, 30 Jun 2020 02:36:59: 1000000 INFO @ Tue, 30 Jun 2020 02:37:00: 5000000 INFO @ Tue, 30 Jun 2020 02:37:07: 2000000 INFO @ Tue, 30 Jun 2020 02:37:09: 6000000 INFO @ Tue, 30 Jun 2020 02:37:16: 3000000 INFO @ Tue, 30 Jun 2020 02:37:17: 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 02:37:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.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 02:37:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:37:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:37:25: 4000000 INFO @ Tue, 30 Jun 2020 02:37:26: 8000000 INFO @ Tue, 30 Jun 2020 02:37:29: 1000000 INFO @ Tue, 30 Jun 2020 02:37:34: 5000000 INFO @ Tue, 30 Jun 2020 02:37:34: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:37:34: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:37:34: #1 total tags in treatment: 8810766 INFO @ Tue, 30 Jun 2020 02:37:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:37:34: #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 02:37:35: #1 tags after filtering in treatment: 8810722 INFO @ Tue, 30 Jun 2020 02:37:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:37:35: #1 finished! INFO @ Tue, 30 Jun 2020 02:37:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:37:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:37:35: #2 number of paired peaks: 393 WARNING @ Tue, 30 Jun 2020 02:37:35: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Tue, 30 Jun 2020 02:37:35: start model_add_line... INFO @ Tue, 30 Jun 2020 02:37:35: start X-correlation... INFO @ Tue, 30 Jun 2020 02:37:35: end of X-cor INFO @ Tue, 30 Jun 2020 02:37:35: #2 finished! INFO @ Tue, 30 Jun 2020 02:37:35: #2 predicted fragment length is 104 bps INFO @ Tue, 30 Jun 2020 02:37:35: #2 alternative fragment length(s) may be 104 bps INFO @ Tue, 30 Jun 2020 02:37:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.05_model.r WARNING @ Tue, 30 Jun 2020 02:37:35: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:37:35: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Tue, 30 Jun 2020 02:37:35: #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 02:37:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:37:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:37:38: 2000000 INFO @ Tue, 30 Jun 2020 02:37:43: 6000000 INFO @ Tue, 30 Jun 2020 02:37:46: 3000000 INFO @ Tue, 30 Jun 2020 02:37:51: 7000000 INFO @ Tue, 30 Jun 2020 02:37:55: 4000000 INFO @ Tue, 30 Jun 2020 02:37:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:38:01: 8000000 INFO @ Tue, 30 Jun 2020 02:38:04: 5000000 INFO @ Tue, 30 Jun 2020 02:38:08: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:38:08: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:38:08: #1 total tags in treatment: 8810766 INFO @ Tue, 30 Jun 2020 02:38:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:38:08: #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 02:38:08: #1 tags after filtering in treatment: 8810722 INFO @ Tue, 30 Jun 2020 02:38:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:38:08: #1 finished! INFO @ Tue, 30 Jun 2020 02:38:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:38:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:38:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:38:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:38:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.05_summits.bed INFO @ Tue, 30 Jun 2020 02:38:09: Done! pass1 - making usageList (515 chroms): 1 millis pass2 - checking and writing primary data (1344 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:38:09: #2 number of paired peaks: 393 WARNING @ Tue, 30 Jun 2020 02:38:09: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Tue, 30 Jun 2020 02:38:09: start model_add_line... INFO @ Tue, 30 Jun 2020 02:38:09: start X-correlation... INFO @ Tue, 30 Jun 2020 02:38:09: end of X-cor INFO @ Tue, 30 Jun 2020 02:38:09: #2 finished! INFO @ Tue, 30 Jun 2020 02:38:09: #2 predicted fragment length is 104 bps INFO @ Tue, 30 Jun 2020 02:38:09: #2 alternative fragment length(s) may be 104 bps INFO @ Tue, 30 Jun 2020 02:38:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.10_model.r WARNING @ Tue, 30 Jun 2020 02:38:09: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:38:09: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Tue, 30 Jun 2020 02:38:09: #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 02:38:09: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:38:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:38:12: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:38:20: 7000000 INFO @ Tue, 30 Jun 2020 02:38:28: 8000000 INFO @ Tue, 30 Jun 2020 02:38:32: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:38:35: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:38:35: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:38:35: #1 total tags in treatment: 8810766 INFO @ Tue, 30 Jun 2020 02:38:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:38:35: #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 02:38:35: #1 tags after filtering in treatment: 8810722 INFO @ Tue, 30 Jun 2020 02:38:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:38:35: #1 finished! INFO @ Tue, 30 Jun 2020 02:38:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:38:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:38:36: #2 number of paired peaks: 393 WARNING @ Tue, 30 Jun 2020 02:38:36: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Tue, 30 Jun 2020 02:38:36: start model_add_line... INFO @ Tue, 30 Jun 2020 02:38:36: start X-correlation... INFO @ Tue, 30 Jun 2020 02:38:36: end of X-cor INFO @ Tue, 30 Jun 2020 02:38:36: #2 finished! INFO @ Tue, 30 Jun 2020 02:38:36: #2 predicted fragment length is 104 bps INFO @ Tue, 30 Jun 2020 02:38:36: #2 alternative fragment length(s) may be 104 bps INFO @ Tue, 30 Jun 2020 02:38:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.20_model.r WARNING @ Tue, 30 Jun 2020 02:38:36: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:38:36: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Tue, 30 Jun 2020 02:38:36: #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 02:38:36: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:38:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:38:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:38:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:38:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.10_summits.bed INFO @ Tue, 30 Jun 2020 02:38:42: Done! pass1 - making usageList (367 chroms): 2 millis pass2 - checking and writing primary data (777 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:38:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:39:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:39:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:39:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511945/SRX3511945.20_summits.bed INFO @ Tue, 30 Jun 2020 02:39:08: Done! pass1 - making usageList (193 chroms): 1 millis pass2 - checking and writing primary data (316 records, 4 fields): 8 millis CompletedMACS2peakCalling