Job ID = 6529825 SRX = SRX495210 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: 00:04:30 17232507 reads; of these: 17232507 (100.00%) were unpaired; of these: 337960 (1.96%) aligned 0 times 12617099 (73.22%) aligned exactly 1 time 4277448 (24.82%) aligned >1 times 98.04% 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] 3805011 / 16894547 = 0.2252 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 02:54:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.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 02:54:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:54:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:54:09: 1000000 INFO @ Tue, 30 Jun 2020 02:54:15: 2000000 INFO @ Tue, 30 Jun 2020 02:54:22: 3000000 INFO @ Tue, 30 Jun 2020 02:54:28: 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 02:54:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.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 02:54:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:54:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:54:34: 5000000 INFO @ Tue, 30 Jun 2020 02:54:39: 1000000 INFO @ Tue, 30 Jun 2020 02:54:42: 6000000 INFO @ Tue, 30 Jun 2020 02:54:45: 2000000 INFO @ Tue, 30 Jun 2020 02:54:49: 7000000 INFO @ Tue, 30 Jun 2020 02:54:51: 3000000 INFO @ Tue, 30 Jun 2020 02:54:56: 8000000 INFO @ Tue, 30 Jun 2020 02:54:57: 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 02:55:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.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 02:55:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:55:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:55:03: 9000000 INFO @ Tue, 30 Jun 2020 02:55:03: 5000000 INFO @ Tue, 30 Jun 2020 02:55:10: 1000000 INFO @ Tue, 30 Jun 2020 02:55:10: 10000000 INFO @ Tue, 30 Jun 2020 02:55:10: 6000000 INFO @ Tue, 30 Jun 2020 02:55:16: 7000000 INFO @ Tue, 30 Jun 2020 02:55:16: 2000000 INFO @ Tue, 30 Jun 2020 02:55:17: 11000000 INFO @ Tue, 30 Jun 2020 02:55:22: 8000000 INFO @ Tue, 30 Jun 2020 02:55:23: 3000000 INFO @ Tue, 30 Jun 2020 02:55:24: 12000000 INFO @ Tue, 30 Jun 2020 02:55:29: 9000000 INFO @ Tue, 30 Jun 2020 02:55:30: 4000000 INFO @ Tue, 30 Jun 2020 02:55:31: 13000000 INFO @ Tue, 30 Jun 2020 02:55:32: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 02:55:32: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 02:55:32: #1 total tags in treatment: 13089536 INFO @ Tue, 30 Jun 2020 02:55:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:55:32: #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 02:55:32: #1 tags after filtering in treatment: 13089536 INFO @ Tue, 30 Jun 2020 02:55:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:55:32: #1 finished! INFO @ Tue, 30 Jun 2020 02:55:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:55:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:55:33: #2 number of paired peaks: 128 WARNING @ Tue, 30 Jun 2020 02:55:33: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 30 Jun 2020 02:55:33: start model_add_line... INFO @ Tue, 30 Jun 2020 02:55:33: start X-correlation... INFO @ Tue, 30 Jun 2020 02:55:33: end of X-cor INFO @ Tue, 30 Jun 2020 02:55:33: #2 finished! INFO @ Tue, 30 Jun 2020 02:55:33: #2 predicted fragment length is 71 bps INFO @ Tue, 30 Jun 2020 02:55:33: #2 alternative fragment length(s) may be 3,10,46,71,527,569,578 bps INFO @ Tue, 30 Jun 2020 02:55:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.05_model.r WARNING @ Tue, 30 Jun 2020 02:55:33: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:55:33: #2 You may need to consider one of the other alternative d(s): 3,10,46,71,527,569,578 WARNING @ Tue, 30 Jun 2020 02:55:33: #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 02:55:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:55:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:55:35: 10000000 INFO @ Tue, 30 Jun 2020 02:55:36: 5000000 INFO @ Tue, 30 Jun 2020 02:55:42: 11000000 INFO @ Tue, 30 Jun 2020 02:55:43: 6000000 INFO @ Tue, 30 Jun 2020 02:55:48: 12000000 INFO @ Tue, 30 Jun 2020 02:55:49: 7000000 INFO @ Tue, 30 Jun 2020 02:55:54: 13000000 INFO @ Tue, 30 Jun 2020 02:55:55: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 02:55:55: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 02:55:55: #1 total tags in treatment: 13089536 INFO @ Tue, 30 Jun 2020 02:55:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:55:55: #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 02:55:56: #1 tags after filtering in treatment: 13089536 INFO @ Tue, 30 Jun 2020 02:55:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:55:56: #1 finished! INFO @ Tue, 30 Jun 2020 02:55:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:55:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:55:56: 8000000 INFO @ Tue, 30 Jun 2020 02:55:56: #2 number of paired peaks: 128 WARNING @ Tue, 30 Jun 2020 02:55:56: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 30 Jun 2020 02:55:56: start model_add_line... INFO @ Tue, 30 Jun 2020 02:55:57: start X-correlation... INFO @ Tue, 30 Jun 2020 02:55:57: end of X-cor INFO @ Tue, 30 Jun 2020 02:55:57: #2 finished! INFO @ Tue, 30 Jun 2020 02:55:57: #2 predicted fragment length is 71 bps INFO @ Tue, 30 Jun 2020 02:55:57: #2 alternative fragment length(s) may be 3,10,46,71,527,569,578 bps INFO @ Tue, 30 Jun 2020 02:55:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.10_model.r WARNING @ Tue, 30 Jun 2020 02:55:57: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:55:57: #2 You may need to consider one of the other alternative d(s): 3,10,46,71,527,569,578 WARNING @ Tue, 30 Jun 2020 02:55:57: #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 02:55:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:55:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:55:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:56:02: 9000000 INFO @ Tue, 30 Jun 2020 02:56:09: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:56:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:56:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:56:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.05_summits.bed INFO @ Tue, 30 Jun 2020 02:56:12: Done! pass1 - making usageList (321 chroms): 1 millis pass2 - checking and writing primary data (646 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:56:15: 11000000 INFO @ Tue, 30 Jun 2020 02:56:22: 12000000 INFO @ Tue, 30 Jun 2020 02:56:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:56:28: 13000000 INFO @ Tue, 30 Jun 2020 02:56:29: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 02:56:29: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 02:56:29: #1 total tags in treatment: 13089536 INFO @ Tue, 30 Jun 2020 02:56:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:56:29: #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 02:56:29: #1 tags after filtering in treatment: 13089536 INFO @ Tue, 30 Jun 2020 02:56:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:56:29: #1 finished! INFO @ Tue, 30 Jun 2020 02:56:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:56:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:56:30: #2 number of paired peaks: 128 WARNING @ Tue, 30 Jun 2020 02:56:30: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 30 Jun 2020 02:56:30: start model_add_line... INFO @ Tue, 30 Jun 2020 02:56:30: start X-correlation... INFO @ Tue, 30 Jun 2020 02:56:30: end of X-cor INFO @ Tue, 30 Jun 2020 02:56:30: #2 finished! INFO @ Tue, 30 Jun 2020 02:56:30: #2 predicted fragment length is 71 bps INFO @ Tue, 30 Jun 2020 02:56:30: #2 alternative fragment length(s) may be 3,10,46,71,527,569,578 bps INFO @ Tue, 30 Jun 2020 02:56:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.20_model.r WARNING @ Tue, 30 Jun 2020 02:56:30: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:56:30: #2 You may need to consider one of the other alternative d(s): 3,10,46,71,527,569,578 WARNING @ Tue, 30 Jun 2020 02:56:30: #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 02:56:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:56:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:56:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:56:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:56:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.10_summits.bed INFO @ Tue, 30 Jun 2020 02:56:35: Done! pass1 - making usageList (108 chroms): 1 millis pass2 - checking and writing primary data (244 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:56:55: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:57:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:57:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:57:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495210/SRX495210.20_summits.bed INFO @ Tue, 30 Jun 2020 02:57:08: Done! pass1 - making usageList (76 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 4 millis CompletedMACS2peakCalling