Job ID = 6529568 SRX = SRX318790 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: 00:04:38 17761171 reads; of these: 17761171 (100.00%) were unpaired; of these: 1061882 (5.98%) aligned 0 times 12962606 (72.98%) aligned exactly 1 time 3736683 (21.04%) aligned >1 times 94.02% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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] 1639514 / 16699289 = 0.0982 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 02:35:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.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 02:35:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:35:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:35:27: 1000000 INFO @ Tue, 30 Jun 2020 02:35:32: 2000000 INFO @ Tue, 30 Jun 2020 02:35:37: 3000000 INFO @ Tue, 30 Jun 2020 02:35:41: 4000000 INFO @ Tue, 30 Jun 2020 02:35:46: 5000000 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 02:35:51: 6000000 INFO @ Tue, 30 Jun 2020 02:35:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.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 02:35:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:35:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:35:56: 7000000 INFO @ Tue, 30 Jun 2020 02:35:58: 1000000 INFO @ Tue, 30 Jun 2020 02:36:01: 8000000 INFO @ Tue, 30 Jun 2020 02:36:03: 2000000 INFO @ Tue, 30 Jun 2020 02:36:06: 9000000 INFO @ Tue, 30 Jun 2020 02:36:09: 3000000 INFO @ Tue, 30 Jun 2020 02:36:12: 10000000 INFO @ Tue, 30 Jun 2020 02:36:15: 4000000 INFO @ Tue, 30 Jun 2020 02:36:17: 11000000 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 02:36:21: 5000000 INFO @ Tue, 30 Jun 2020 02:36:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.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 02:36:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:36:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:36:22: 12000000 INFO @ Tue, 30 Jun 2020 02:36:27: 6000000 INFO @ Tue, 30 Jun 2020 02:36:28: 13000000 INFO @ Tue, 30 Jun 2020 02:36:28: 1000000 INFO @ Tue, 30 Jun 2020 02:36:33: 14000000 INFO @ Tue, 30 Jun 2020 02:36:33: 7000000 INFO @ Tue, 30 Jun 2020 02:36:35: 2000000 INFO @ Tue, 30 Jun 2020 02:36:38: 15000000 INFO @ Tue, 30 Jun 2020 02:36:39: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:36:39: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:36:39: #1 total tags in treatment: 15059775 INFO @ Tue, 30 Jun 2020 02:36:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:36:39: #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 02:36:39: #1 tags after filtering in treatment: 15059774 INFO @ Tue, 30 Jun 2020 02:36:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:36:39: #1 finished! INFO @ Tue, 30 Jun 2020 02:36:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:36:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:36:39: 8000000 INFO @ Tue, 30 Jun 2020 02:36:40: #2 number of paired peaks: 331 WARNING @ Tue, 30 Jun 2020 02:36:40: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Tue, 30 Jun 2020 02:36:40: start model_add_line... INFO @ Tue, 30 Jun 2020 02:36:40: start X-correlation... INFO @ Tue, 30 Jun 2020 02:36:40: end of X-cor INFO @ Tue, 30 Jun 2020 02:36:40: #2 finished! INFO @ Tue, 30 Jun 2020 02:36:40: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:36:40: #2 alternative fragment length(s) may be 4,45,549,566 bps INFO @ Tue, 30 Jun 2020 02:36:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.05_model.r WARNING @ Tue, 30 Jun 2020 02:36:40: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:36:40: #2 You may need to consider one of the other alternative d(s): 4,45,549,566 WARNING @ Tue, 30 Jun 2020 02:36:40: #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 02:36:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:36:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:36:41: 3000000 INFO @ Tue, 30 Jun 2020 02:36:45: 9000000 INFO @ Tue, 30 Jun 2020 02:36:47: 4000000 INFO @ Tue, 30 Jun 2020 02:36:52: 10000000 INFO @ Tue, 30 Jun 2020 02:36:54: 5000000 INFO @ Tue, 30 Jun 2020 02:36:58: 11000000 INFO @ Tue, 30 Jun 2020 02:37:00: 6000000 INFO @ Tue, 30 Jun 2020 02:37:05: 12000000 INFO @ Tue, 30 Jun 2020 02:37:06: 7000000 INFO @ Tue, 30 Jun 2020 02:37:08: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:37:12: 8000000 INFO @ Tue, 30 Jun 2020 02:37:12: 13000000 INFO @ Tue, 30 Jun 2020 02:37:18: 9000000 INFO @ Tue, 30 Jun 2020 02:37:19: 14000000 INFO @ Tue, 30 Jun 2020 02:37:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:37:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:37:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.05_summits.bed INFO @ Tue, 30 Jun 2020 02:37:22: Done! pass1 - making usageList (517 chroms): 1 millis pass2 - checking and writing primary data (2022 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:37:24: 10000000 INFO @ Tue, 30 Jun 2020 02:37:25: 15000000 INFO @ Tue, 30 Jun 2020 02:37:26: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:37:26: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:37:26: #1 total tags in treatment: 15059775 INFO @ Tue, 30 Jun 2020 02:37:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:37:26: #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 02:37:26: #1 tags after filtering in treatment: 15059774 INFO @ Tue, 30 Jun 2020 02:37:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:37:26: #1 finished! INFO @ Tue, 30 Jun 2020 02:37:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:37:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:37:27: #2 number of paired peaks: 331 WARNING @ Tue, 30 Jun 2020 02:37:27: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Tue, 30 Jun 2020 02:37:27: start model_add_line... INFO @ Tue, 30 Jun 2020 02:37:28: start X-correlation... INFO @ Tue, 30 Jun 2020 02:37:28: end of X-cor INFO @ Tue, 30 Jun 2020 02:37:28: #2 finished! INFO @ Tue, 30 Jun 2020 02:37:28: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:37:28: #2 alternative fragment length(s) may be 4,45,549,566 bps INFO @ Tue, 30 Jun 2020 02:37:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.10_model.r WARNING @ Tue, 30 Jun 2020 02:37:28: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:37:28: #2 You may need to consider one of the other alternative d(s): 4,45,549,566 WARNING @ Tue, 30 Jun 2020 02:37:28: #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 02:37:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:37:28: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:37:30: 11000000 INFO @ Tue, 30 Jun 2020 02:37:36: 12000000 INFO @ Tue, 30 Jun 2020 02:37:42: 13000000 INFO @ Tue, 30 Jun 2020 02:37:48: 14000000 INFO @ Tue, 30 Jun 2020 02:37:54: 15000000 INFO @ Tue, 30 Jun 2020 02:37:54: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:37:54: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:37:54: #1 total tags in treatment: 15059775 INFO @ Tue, 30 Jun 2020 02:37:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:37:54: #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 02:37:55: #1 tags after filtering in treatment: 15059774 INFO @ Tue, 30 Jun 2020 02:37:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:37:55: #1 finished! INFO @ Tue, 30 Jun 2020 02:37:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:37:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:37:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:37:56: #2 number of paired peaks: 331 WARNING @ Tue, 30 Jun 2020 02:37:56: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Tue, 30 Jun 2020 02:37:56: start model_add_line... INFO @ Tue, 30 Jun 2020 02:37:56: start X-correlation... INFO @ Tue, 30 Jun 2020 02:37:56: end of X-cor INFO @ Tue, 30 Jun 2020 02:37:56: #2 finished! INFO @ Tue, 30 Jun 2020 02:37:56: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 02:37:56: #2 alternative fragment length(s) may be 4,45,549,566 bps INFO @ Tue, 30 Jun 2020 02:37:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.20_model.r WARNING @ Tue, 30 Jun 2020 02:37:56: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:37:56: #2 You may need to consider one of the other alternative d(s): 4,45,549,566 WARNING @ Tue, 30 Jun 2020 02:37:56: #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 02:37:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:37:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:38:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:38:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:38:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.10_summits.bed INFO @ Tue, 30 Jun 2020 02:38:09: Done! pass1 - making usageList (447 chroms): 1 millis pass2 - checking and writing primary data (1648 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:38:24: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:38:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:38:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:38:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318790/SRX318790.20_summits.bed INFO @ Tue, 30 Jun 2020 02:38:37: Done! pass1 - making usageList (271 chroms): 1 millis pass2 - checking and writing primary data (522 records, 4 fields): 10 millis CompletedMACS2peakCalling