Job ID = 6529275 SRX = SRX1166571 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: 00:05:44 25367465 reads; of these: 25367465 (100.00%) were unpaired; of these: 511646 (2.02%) aligned 0 times 19785775 (78.00%) aligned exactly 1 time 5070044 (19.99%) aligned >1 times 97.98% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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 12 files... [bam_rmdupse_core] 8253651 / 24855819 = 0.3321 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 02:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.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 02:08:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:08:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:08:15: 1000000 INFO @ Tue, 30 Jun 2020 02:08:21: 2000000 INFO @ Tue, 30 Jun 2020 02:08:28: 3000000 INFO @ Tue, 30 Jun 2020 02:08:34: 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 02:08:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.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 02:08:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:08:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:08:40: 5000000 INFO @ Tue, 30 Jun 2020 02:08:45: 1000000 INFO @ Tue, 30 Jun 2020 02:08:47: 6000000 INFO @ Tue, 30 Jun 2020 02:08:52: 2000000 INFO @ Tue, 30 Jun 2020 02:08:53: 7000000 INFO @ Tue, 30 Jun 2020 02:08:58: 3000000 INFO @ Tue, 30 Jun 2020 02:09:00: 8000000 INFO @ Tue, 30 Jun 2020 02:09:05: 4000000 INFO @ Tue, 30 Jun 2020 02:09:06: 9000000 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 02:09:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.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 02:09:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:09:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:09:11: 5000000 INFO @ Tue, 30 Jun 2020 02:09:12: 10000000 INFO @ Tue, 30 Jun 2020 02:09:15: 1000000 INFO @ Tue, 30 Jun 2020 02:09:18: 6000000 INFO @ Tue, 30 Jun 2020 02:09:19: 11000000 INFO @ Tue, 30 Jun 2020 02:09:21: 2000000 INFO @ Tue, 30 Jun 2020 02:09:24: 7000000 INFO @ Tue, 30 Jun 2020 02:09:25: 12000000 INFO @ Tue, 30 Jun 2020 02:09:27: 3000000 INFO @ Tue, 30 Jun 2020 02:09:31: 8000000 INFO @ Tue, 30 Jun 2020 02:09:32: 13000000 INFO @ Tue, 30 Jun 2020 02:09:33: 4000000 INFO @ Tue, 30 Jun 2020 02:09:37: 9000000 INFO @ Tue, 30 Jun 2020 02:09:39: 14000000 INFO @ Tue, 30 Jun 2020 02:09:40: 5000000 INFO @ Tue, 30 Jun 2020 02:09:44: 10000000 INFO @ Tue, 30 Jun 2020 02:09:45: 15000000 INFO @ Tue, 30 Jun 2020 02:09:46: 6000000 INFO @ Tue, 30 Jun 2020 02:09:50: 11000000 INFO @ Tue, 30 Jun 2020 02:09:51: 16000000 INFO @ Tue, 30 Jun 2020 02:09:52: 7000000 INFO @ Tue, 30 Jun 2020 02:09:55: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:09:55: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:09:55: #1 total tags in treatment: 16602168 INFO @ Tue, 30 Jun 2020 02:09:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:09:55: #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 02:09:56: #1 tags after filtering in treatment: 16602091 INFO @ Tue, 30 Jun 2020 02:09:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:09:56: #1 finished! INFO @ Tue, 30 Jun 2020 02:09:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:09:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:09:56: 12000000 INFO @ Tue, 30 Jun 2020 02:09:57: #2 number of paired peaks: 353 WARNING @ Tue, 30 Jun 2020 02:09:57: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Tue, 30 Jun 2020 02:09:57: start model_add_line... INFO @ Tue, 30 Jun 2020 02:09:57: start X-correlation... INFO @ Tue, 30 Jun 2020 02:09:57: end of X-cor INFO @ Tue, 30 Jun 2020 02:09:57: #2 finished! INFO @ Tue, 30 Jun 2020 02:09:57: #2 predicted fragment length is 58 bps INFO @ Tue, 30 Jun 2020 02:09:57: #2 alternative fragment length(s) may be 4,58 bps INFO @ Tue, 30 Jun 2020 02:09:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.05_model.r WARNING @ Tue, 30 Jun 2020 02:09:57: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:09:57: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Tue, 30 Jun 2020 02:09:57: #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 02:09:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:09:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:09:58: 8000000 INFO @ Tue, 30 Jun 2020 02:10:03: 13000000 INFO @ Tue, 30 Jun 2020 02:10:05: 9000000 INFO @ Tue, 30 Jun 2020 02:10:10: 14000000 INFO @ Tue, 30 Jun 2020 02:10:11: 10000000 INFO @ Tue, 30 Jun 2020 02:10:16: 15000000 INFO @ Tue, 30 Jun 2020 02:10:17: 11000000 INFO @ Tue, 30 Jun 2020 02:10:22: 16000000 INFO @ Tue, 30 Jun 2020 02:10:23: 12000000 INFO @ Tue, 30 Jun 2020 02:10:26: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:10:26: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:10:26: #1 total tags in treatment: 16602168 INFO @ Tue, 30 Jun 2020 02:10:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:10:26: #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 02:10:27: #1 tags after filtering in treatment: 16602091 INFO @ Tue, 30 Jun 2020 02:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:10:27: #1 finished! INFO @ Tue, 30 Jun 2020 02:10:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:10:28: #2 number of paired peaks: 353 WARNING @ Tue, 30 Jun 2020 02:10:28: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Tue, 30 Jun 2020 02:10:28: start model_add_line... INFO @ Tue, 30 Jun 2020 02:10:28: start X-correlation... INFO @ Tue, 30 Jun 2020 02:10:28: end of X-cor INFO @ Tue, 30 Jun 2020 02:10:28: #2 finished! INFO @ Tue, 30 Jun 2020 02:10:28: #2 predicted fragment length is 58 bps INFO @ Tue, 30 Jun 2020 02:10:28: #2 alternative fragment length(s) may be 4,58 bps INFO @ Tue, 30 Jun 2020 02:10:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.10_model.r WARNING @ Tue, 30 Jun 2020 02:10:28: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:10:28: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Tue, 30 Jun 2020 02:10:28: #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 02:10:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:10:28: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:10:29: 13000000 INFO @ Tue, 30 Jun 2020 02:10:32: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:10:34: 14000000 INFO @ Tue, 30 Jun 2020 02:10:40: 15000000 INFO @ Tue, 30 Jun 2020 02:10:45: 16000000 INFO @ Tue, 30 Jun 2020 02:10:49: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:10:49: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:10:49: #1 total tags in treatment: 16602168 INFO @ Tue, 30 Jun 2020 02:10:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:10:49: #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 02:10:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:10:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:10:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.05_summits.bed INFO @ Tue, 30 Jun 2020 02:10:49: Done! pass1 - making usageList (513 chroms): 2 millis pass2 - checking and writing primary data (2187 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:10:49: #1 tags after filtering in treatment: 16602091 INFO @ Tue, 30 Jun 2020 02:10:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:10:49: #1 finished! INFO @ Tue, 30 Jun 2020 02:10:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:10:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:10:50: #2 number of paired peaks: 353 WARNING @ Tue, 30 Jun 2020 02:10:50: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Tue, 30 Jun 2020 02:10:50: start model_add_line... INFO @ Tue, 30 Jun 2020 02:10:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:10:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:10:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:10:51: #2 predicted fragment length is 58 bps INFO @ Tue, 30 Jun 2020 02:10:51: #2 alternative fragment length(s) may be 4,58 bps INFO @ Tue, 30 Jun 2020 02:10:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.20_model.r WARNING @ Tue, 30 Jun 2020 02:10:51: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:10:51: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Tue, 30 Jun 2020 02:10:51: #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 02:10:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:10:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:11:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:11:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:11:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:11:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.10_summits.bed INFO @ Tue, 30 Jun 2020 02:11:19: Done! pass1 - making usageList (368 chroms): 1 millis pass2 - checking and writing primary data (1055 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:11:27: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:11:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:11:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:11:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1166571/SRX1166571.20_summits.bed INFO @ Tue, 30 Jun 2020 02:11:44: Done! pass1 - making usageList (135 chroms): 1 millis pass2 - checking and writing primary data (340 records, 4 fields): 6 millis CompletedMACS2peakCalling