Job ID = 6529772 SRX = SRX474595 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: 00:04:31 16032574 reads; of these: 16032574 (100.00%) were unpaired; of these: 858923 (5.36%) aligned 0 times 10806691 (67.40%) aligned exactly 1 time 4366960 (27.24%) aligned >1 times 94.64% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 3163898 / 15173651 = 0.2085 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 02:51:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.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 02:51:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:51:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:51:32: 1000000 INFO @ Tue, 30 Jun 2020 02:51:38: 2000000 INFO @ Tue, 30 Jun 2020 02:51:44: 3000000 INFO @ Tue, 30 Jun 2020 02:51:50: 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 02:51:56: 5000000 INFO @ Tue, 30 Jun 2020 02:51:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.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 02:51:58: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:51:58: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:03: 6000000 INFO @ Tue, 30 Jun 2020 02:52:04: 1000000 INFO @ Tue, 30 Jun 2020 02:52:09: 7000000 INFO @ Tue, 30 Jun 2020 02:52:11: 2000000 INFO @ Tue, 30 Jun 2020 02:52:15: 8000000 INFO @ Tue, 30 Jun 2020 02:52:17: 3000000 INFO @ Tue, 30 Jun 2020 02:52:22: 9000000 INFO @ Tue, 30 Jun 2020 02:52:24: 4000000 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 02:52:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.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 02:52:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:29: 10000000 INFO @ Tue, 30 Jun 2020 02:52:30: 5000000 INFO @ Tue, 30 Jun 2020 02:52:33: 1000000 INFO @ Tue, 30 Jun 2020 02:52:35: 11000000 INFO @ Tue, 30 Jun 2020 02:52:37: 6000000 INFO @ Tue, 30 Jun 2020 02:52:40: 2000000 INFO @ Tue, 30 Jun 2020 02:52:42: 12000000 INFO @ Tue, 30 Jun 2020 02:52:42: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:52:42: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:52:42: #1 total tags in treatment: 12009753 INFO @ Tue, 30 Jun 2020 02:52:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:52:42: #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 02:52:43: #1 tags after filtering in treatment: 12009747 INFO @ Tue, 30 Jun 2020 02:52:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:52:43: #1 finished! INFO @ Tue, 30 Jun 2020 02:52:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:52:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:52:43: 7000000 INFO @ Tue, 30 Jun 2020 02:52:43: #2 number of paired peaks: 116 WARNING @ Tue, 30 Jun 2020 02:52:43: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Tue, 30 Jun 2020 02:52:43: start model_add_line... INFO @ Tue, 30 Jun 2020 02:52:43: start X-correlation... INFO @ Tue, 30 Jun 2020 02:52:43: end of X-cor INFO @ Tue, 30 Jun 2020 02:52:43: #2 finished! INFO @ Tue, 30 Jun 2020 02:52:43: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:52:43: #2 alternative fragment length(s) may be 3,44,547 bps INFO @ Tue, 30 Jun 2020 02:52:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.05_model.r WARNING @ Tue, 30 Jun 2020 02:52:43: #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 02:52:43: #2 You may need to consider one of the other alternative d(s): 3,44,547 WARNING @ Tue, 30 Jun 2020 02:52:43: #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 02:52:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:52:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:52:46: 3000000 INFO @ Tue, 30 Jun 2020 02:52:50: 8000000 INFO @ Tue, 30 Jun 2020 02:52:52: 4000000 INFO @ Tue, 30 Jun 2020 02:52:56: 9000000 INFO @ Tue, 30 Jun 2020 02:52:59: 5000000 INFO @ Tue, 30 Jun 2020 02:53:03: 10000000 INFO @ Tue, 30 Jun 2020 02:53:05: 6000000 INFO @ Tue, 30 Jun 2020 02:53:09: 11000000 INFO @ Tue, 30 Jun 2020 02:53:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:53:12: 7000000 INFO @ Tue, 30 Jun 2020 02:53:16: 12000000 INFO @ Tue, 30 Jun 2020 02:53:16: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:53:16: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:53:16: #1 total tags in treatment: 12009753 INFO @ Tue, 30 Jun 2020 02:53:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:53:16: #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 02:53:16: #1 tags after filtering in treatment: 12009747 INFO @ Tue, 30 Jun 2020 02:53:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:53:16: #1 finished! INFO @ Tue, 30 Jun 2020 02:53:16: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:53:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:53:17: #2 number of paired peaks: 116 WARNING @ Tue, 30 Jun 2020 02:53:17: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Tue, 30 Jun 2020 02:53:17: start model_add_line... INFO @ Tue, 30 Jun 2020 02:53:17: start X-correlation... INFO @ Tue, 30 Jun 2020 02:53:17: end of X-cor INFO @ Tue, 30 Jun 2020 02:53:17: #2 finished! INFO @ Tue, 30 Jun 2020 02:53:17: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:53:17: #2 alternative fragment length(s) may be 3,44,547 bps INFO @ Tue, 30 Jun 2020 02:53:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.10_model.r WARNING @ Tue, 30 Jun 2020 02:53:17: #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 02:53:17: #2 You may need to consider one of the other alternative d(s): 3,44,547 WARNING @ Tue, 30 Jun 2020 02:53:17: #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 02:53:17: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:53:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:53:18: 8000000 INFO @ Tue, 30 Jun 2020 02:53:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:53:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:53:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.05_summits.bed INFO @ Tue, 30 Jun 2020 02:53:23: Done! pass1 - making usageList (533 chroms): 1 millis pass2 - checking and writing primary data (1732 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:53:24: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:53:30: 10000000 INFO @ Tue, 30 Jun 2020 02:53:36: 11000000 INFO @ Tue, 30 Jun 2020 02:53:42: 12000000 INFO @ Tue, 30 Jun 2020 02:53:42: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:53:42: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:53:42: #1 total tags in treatment: 12009753 INFO @ Tue, 30 Jun 2020 02:53:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:53:42: #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 02:53:43: #1 tags after filtering in treatment: 12009747 INFO @ Tue, 30 Jun 2020 02:53:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:53:43: #1 finished! INFO @ Tue, 30 Jun 2020 02:53:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:53:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:53:43: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:53:44: #2 number of paired peaks: 116 WARNING @ Tue, 30 Jun 2020 02:53:44: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Tue, 30 Jun 2020 02:53:44: start model_add_line... INFO @ Tue, 30 Jun 2020 02:53:44: start X-correlation... INFO @ Tue, 30 Jun 2020 02:53:44: end of X-cor INFO @ Tue, 30 Jun 2020 02:53:44: #2 finished! INFO @ Tue, 30 Jun 2020 02:53:44: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 02:53:44: #2 alternative fragment length(s) may be 3,44,547 bps INFO @ Tue, 30 Jun 2020 02:53:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.20_model.r WARNING @ Tue, 30 Jun 2020 02:53:44: #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 02:53:44: #2 You may need to consider one of the other alternative d(s): 3,44,547 WARNING @ Tue, 30 Jun 2020 02:53:44: #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 02:53:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:53:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:53:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:53:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:53:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.10_summits.bed INFO @ Tue, 30 Jun 2020 02:53:56: Done! pass1 - making usageList (141 chroms): 1 millis pass2 - checking and writing primary data (274 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:54:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:54:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:54:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:54:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474595/SRX474595.20_summits.bed INFO @ Tue, 30 Jun 2020 02:54:22: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (110 records, 4 fields): 3 millis CompletedMACS2peakCalling