Job ID = 6529352 SRX = SRX2011093 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: 00:06:25 15156147 reads; of these: 15156147 (100.00%) were unpaired; of these: 546846 (3.61%) aligned 0 times 12923225 (85.27%) aligned exactly 1 time 1686076 (11.12%) aligned >1 times 96.39% overall alignment rate Time searching: 00:06:25 Overall time: 00:06:25 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] 1008683 / 14609301 = 0.0690 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 02:40:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.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 02:40:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:40:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:40:08: 1000000 INFO @ Tue, 30 Jun 2020 02:40:15: 2000000 INFO @ Tue, 30 Jun 2020 02:40:21: 3000000 INFO @ Tue, 30 Jun 2020 02:40:28: 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 02:40:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.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 02:40:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:40:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:40:35: 5000000 INFO @ Tue, 30 Jun 2020 02:40:39: 1000000 INFO @ Tue, 30 Jun 2020 02:40:42: 6000000 INFO @ Tue, 30 Jun 2020 02:40:46: 2000000 INFO @ Tue, 30 Jun 2020 02:40:49: 7000000 INFO @ Tue, 30 Jun 2020 02:40:54: 3000000 INFO @ Tue, 30 Jun 2020 02:40:57: 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 02:41:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.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 02:41:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:41:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:41:01: 4000000 INFO @ Tue, 30 Jun 2020 02:41:04: 9000000 INFO @ Tue, 30 Jun 2020 02:41:10: 5000000 INFO @ Tue, 30 Jun 2020 02:41:10: 1000000 INFO @ Tue, 30 Jun 2020 02:41:13: 10000000 INFO @ Tue, 30 Jun 2020 02:41:18: 6000000 INFO @ Tue, 30 Jun 2020 02:41:19: 2000000 INFO @ Tue, 30 Jun 2020 02:41:21: 11000000 INFO @ Tue, 30 Jun 2020 02:41:26: 7000000 INFO @ Tue, 30 Jun 2020 02:41:28: 3000000 INFO @ Tue, 30 Jun 2020 02:41:29: 12000000 INFO @ Tue, 30 Jun 2020 02:41:34: 8000000 INFO @ Tue, 30 Jun 2020 02:41:36: 4000000 INFO @ Tue, 30 Jun 2020 02:41:37: 13000000 INFO @ Tue, 30 Jun 2020 02:41:42: 9000000 INFO @ Tue, 30 Jun 2020 02:41:42: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:41:42: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:41:42: #1 total tags in treatment: 13600618 INFO @ Tue, 30 Jun 2020 02:41:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:41:42: #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 02:41:43: #1 tags after filtering in treatment: 13600477 INFO @ Tue, 30 Jun 2020 02:41:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:41:43: #1 finished! INFO @ Tue, 30 Jun 2020 02:41:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:41:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:41:44: #2 number of paired peaks: 109 WARNING @ Tue, 30 Jun 2020 02:41:44: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 30 Jun 2020 02:41:44: start model_add_line... INFO @ Tue, 30 Jun 2020 02:41:44: start X-correlation... INFO @ Tue, 30 Jun 2020 02:41:44: end of X-cor INFO @ Tue, 30 Jun 2020 02:41:44: #2 finished! INFO @ Tue, 30 Jun 2020 02:41:44: #2 predicted fragment length is 99 bps INFO @ Tue, 30 Jun 2020 02:41:44: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 30 Jun 2020 02:41:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.05_model.r WARNING @ Tue, 30 Jun 2020 02:41:44: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:41:44: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Tue, 30 Jun 2020 02:41:44: #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 02:41:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:41:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:41:45: 5000000 INFO @ Tue, 30 Jun 2020 02:41:50: 10000000 INFO @ Tue, 30 Jun 2020 02:41:54: 6000000 INFO @ Tue, 30 Jun 2020 02:41:59: 11000000 INFO @ Tue, 30 Jun 2020 02:42:03: 7000000 INFO @ Tue, 30 Jun 2020 02:42:07: 12000000 INFO @ Tue, 30 Jun 2020 02:42:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:42:11: 8000000 INFO @ Tue, 30 Jun 2020 02:42:15: 13000000 INFO @ Tue, 30 Jun 2020 02:42:20: 9000000 INFO @ Tue, 30 Jun 2020 02:42:21: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:42:21: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:42:21: #1 total tags in treatment: 13600618 INFO @ Tue, 30 Jun 2020 02:42:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:42:21: #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 02:42:21: #1 tags after filtering in treatment: 13600477 INFO @ Tue, 30 Jun 2020 02:42:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:42:21: #1 finished! INFO @ Tue, 30 Jun 2020 02:42:21: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:42:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:42:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:42:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:42:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.05_summits.bed INFO @ Tue, 30 Jun 2020 02:42:22: Done! INFO @ Tue, 30 Jun 2020 02:42:22: #2 number of paired peaks: 109 WARNING @ Tue, 30 Jun 2020 02:42:22: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 30 Jun 2020 02:42:22: start model_add_line... INFO @ Tue, 30 Jun 2020 02:42:22: start X-correlation... INFO @ Tue, 30 Jun 2020 02:42:22: end of X-cor INFO @ Tue, 30 Jun 2020 02:42:22: #2 finished! INFO @ Tue, 30 Jun 2020 02:42:22: #2 predicted fragment length is 99 bps INFO @ Tue, 30 Jun 2020 02:42:22: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 30 Jun 2020 02:42:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.10_model.r WARNING @ Tue, 30 Jun 2020 02:42:22: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:42:22: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Tue, 30 Jun 2020 02:42:22: #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 02:42:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:42:22: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (250 chroms): 2 millis pass2 - checking and writing primary data (4707 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:42:29: 10000000 INFO @ Tue, 30 Jun 2020 02:42:37: 11000000 INFO @ Tue, 30 Jun 2020 02:42:46: 12000000 INFO @ Tue, 30 Jun 2020 02:42:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:42:55: 13000000 INFO @ Tue, 30 Jun 2020 02:43:00: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:43:00: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:43:00: #1 total tags in treatment: 13600618 INFO @ Tue, 30 Jun 2020 02:43:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:43:00: #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 02:43:00: #1 tags after filtering in treatment: 13600477 INFO @ Tue, 30 Jun 2020 02:43:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:43:00: #1 finished! INFO @ Tue, 30 Jun 2020 02:43:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:43:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:43:01: #2 number of paired peaks: 109 WARNING @ Tue, 30 Jun 2020 02:43:01: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Tue, 30 Jun 2020 02:43:01: start model_add_line... INFO @ Tue, 30 Jun 2020 02:43:01: start X-correlation... INFO @ Tue, 30 Jun 2020 02:43:01: end of X-cor INFO @ Tue, 30 Jun 2020 02:43:01: #2 finished! INFO @ Tue, 30 Jun 2020 02:43:01: #2 predicted fragment length is 99 bps INFO @ Tue, 30 Jun 2020 02:43:01: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 30 Jun 2020 02:43:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.20_model.r WARNING @ Tue, 30 Jun 2020 02:43:01: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:43:01: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Tue, 30 Jun 2020 02:43:01: #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 02:43:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:43:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:43:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:43:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:43:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.10_summits.bed INFO @ Tue, 30 Jun 2020 02:43:03: Done! pass1 - making usageList (186 chroms): 1 millis pass2 - checking and writing primary data (715 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:43:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:43:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:43:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:43:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2011093/SRX2011093.20_summits.bed INFO @ Tue, 30 Jun 2020 02:43:38: Done! pass1 - making usageList (113 chroms): 1 millis pass2 - checking and writing primary data (211 records, 4 fields): 3 millis CompletedMACS2peakCalling