Job ID = 6528461 SRX = SRX6811508 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T15:11:07 prefetch.2.10.7: 1) Downloading 'SRR10078144'... 2020-06-29T15:11:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:14:16 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:14:16 prefetch.2.10.7: 1) 'SRR10078144' was downloaded successfully Read 28904776 spots for SRR10078144/SRR10078144.sra Written 28904776 spots for SRR10078144/SRR10078144.sra 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:47 28904776 reads; of these: 28904776 (100.00%) were unpaired; of these: 895786 (3.10%) aligned 0 times 19133897 (66.20%) aligned exactly 1 time 8875093 (30.70%) aligned >1 times 96.90% overall alignment rate Time searching: 00:10:48 Overall time: 00:10:48 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4428416 / 28008990 = 0.1581 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 00:40:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.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 00:40:37: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:40:37: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:40:44: 1000000 INFO @ Tue, 30 Jun 2020 00:40:51: 2000000 INFO @ Tue, 30 Jun 2020 00:40:58: 3000000 INFO @ Tue, 30 Jun 2020 00:41:05: 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 00:41:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.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 00:41:07: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:41:07: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:41:12: 5000000 INFO @ Tue, 30 Jun 2020 00:41:14: 1000000 INFO @ Tue, 30 Jun 2020 00:41:19: 6000000 INFO @ Tue, 30 Jun 2020 00:41:22: 2000000 INFO @ Tue, 30 Jun 2020 00:41:27: 7000000 INFO @ Tue, 30 Jun 2020 00:41:29: 3000000 INFO @ Tue, 30 Jun 2020 00:41:35: 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 00:41:36: 4000000 INFO @ Tue, 30 Jun 2020 00:41:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.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 00:41:37: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:41:37: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:41:42: 9000000 INFO @ Tue, 30 Jun 2020 00:41:44: 5000000 INFO @ Tue, 30 Jun 2020 00:41:44: 1000000 INFO @ Tue, 30 Jun 2020 00:41:50: 10000000 INFO @ Tue, 30 Jun 2020 00:41:52: 6000000 INFO @ Tue, 30 Jun 2020 00:41:52: 2000000 INFO @ Tue, 30 Jun 2020 00:41:58: 11000000 INFO @ Tue, 30 Jun 2020 00:42:00: 3000000 INFO @ Tue, 30 Jun 2020 00:42:00: 7000000 INFO @ Tue, 30 Jun 2020 00:42:06: 12000000 INFO @ Tue, 30 Jun 2020 00:42:07: 4000000 INFO @ Tue, 30 Jun 2020 00:42:08: 8000000 INFO @ Tue, 30 Jun 2020 00:42:14: 13000000 INFO @ Tue, 30 Jun 2020 00:42:15: 5000000 INFO @ Tue, 30 Jun 2020 00:42:15: 9000000 INFO @ Tue, 30 Jun 2020 00:42:23: 14000000 INFO @ Tue, 30 Jun 2020 00:42:23: 6000000 INFO @ Tue, 30 Jun 2020 00:42:24: 10000000 INFO @ Tue, 30 Jun 2020 00:42:31: 15000000 INFO @ Tue, 30 Jun 2020 00:42:31: 7000000 INFO @ Tue, 30 Jun 2020 00:42:32: 11000000 INFO @ Tue, 30 Jun 2020 00:42:39: 16000000 INFO @ Tue, 30 Jun 2020 00:42:39: 8000000 INFO @ Tue, 30 Jun 2020 00:42:40: 12000000 INFO @ Tue, 30 Jun 2020 00:42:47: 9000000 INFO @ Tue, 30 Jun 2020 00:42:48: 17000000 INFO @ Tue, 30 Jun 2020 00:42:48: 13000000 INFO @ Tue, 30 Jun 2020 00:42:55: 10000000 INFO @ Tue, 30 Jun 2020 00:42:56: 18000000 INFO @ Tue, 30 Jun 2020 00:42:57: 14000000 INFO @ Tue, 30 Jun 2020 00:43:03: 11000000 INFO @ Tue, 30 Jun 2020 00:43:04: 19000000 INFO @ Tue, 30 Jun 2020 00:43:05: 15000000 INFO @ Tue, 30 Jun 2020 00:43:11: 12000000 INFO @ Tue, 30 Jun 2020 00:43:12: 20000000 INFO @ Tue, 30 Jun 2020 00:43:13: 16000000 INFO @ Tue, 30 Jun 2020 00:43:19: 13000000 INFO @ Tue, 30 Jun 2020 00:43:20: 21000000 INFO @ Tue, 30 Jun 2020 00:43:22: 17000000 INFO @ Tue, 30 Jun 2020 00:43:27: 14000000 INFO @ Tue, 30 Jun 2020 00:43:29: 22000000 INFO @ Tue, 30 Jun 2020 00:43:30: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:43:35: 15000000 INFO @ Tue, 30 Jun 2020 00:43:37: 23000000 INFO @ Tue, 30 Jun 2020 00:43:38: 19000000 INFO @ Tue, 30 Jun 2020 00:43:41: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:43:41: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:43:41: #1 total tags in treatment: 23580574 INFO @ Tue, 30 Jun 2020 00:43:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:43:41: #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 00:43:42: #1 tags after filtering in treatment: 23580574 INFO @ Tue, 30 Jun 2020 00:43:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:43:42: #1 finished! INFO @ Tue, 30 Jun 2020 00:43:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:43:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:43:43: 16000000 INFO @ Tue, 30 Jun 2020 00:43:43: #2 number of paired peaks: 249 WARNING @ Tue, 30 Jun 2020 00:43:43: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Tue, 30 Jun 2020 00:43:43: start model_add_line... INFO @ Tue, 30 Jun 2020 00:43:44: start X-correlation... INFO @ Tue, 30 Jun 2020 00:43:44: end of X-cor INFO @ Tue, 30 Jun 2020 00:43:44: #2 finished! INFO @ Tue, 30 Jun 2020 00:43:44: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 00:43:44: #2 alternative fragment length(s) may be 2,51 bps INFO @ Tue, 30 Jun 2020 00:43:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.05_model.r WARNING @ Tue, 30 Jun 2020 00:43:44: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:43:44: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Tue, 30 Jun 2020 00:43:44: #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 00:43:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:43:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:43:46: 20000000 INFO @ Tue, 30 Jun 2020 00:43:51: 17000000 INFO @ Tue, 30 Jun 2020 00:43:54: 21000000 INFO @ Tue, 30 Jun 2020 00:43:59: 18000000 INFO @ Tue, 30 Jun 2020 00:44:02: 22000000 INFO @ Tue, 30 Jun 2020 00:44:07: 19000000 INFO @ Tue, 30 Jun 2020 00:44:10: 23000000 INFO @ Tue, 30 Jun 2020 00:44:14: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:44:14: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:44:14: #1 total tags in treatment: 23580574 INFO @ Tue, 30 Jun 2020 00:44:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:44:14: #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 00:44:14: 20000000 INFO @ Tue, 30 Jun 2020 00:44:15: #1 tags after filtering in treatment: 23580574 INFO @ Tue, 30 Jun 2020 00:44:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:44:15: #1 finished! INFO @ Tue, 30 Jun 2020 00:44:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:44:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:44:16: #2 number of paired peaks: 249 WARNING @ Tue, 30 Jun 2020 00:44:16: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Tue, 30 Jun 2020 00:44:16: start model_add_line... INFO @ Tue, 30 Jun 2020 00:44:16: start X-correlation... INFO @ Tue, 30 Jun 2020 00:44:16: end of X-cor INFO @ Tue, 30 Jun 2020 00:44:16: #2 finished! INFO @ Tue, 30 Jun 2020 00:44:16: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 00:44:16: #2 alternative fragment length(s) may be 2,51 bps INFO @ Tue, 30 Jun 2020 00:44:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.10_model.r WARNING @ Tue, 30 Jun 2020 00:44:16: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:44:16: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Tue, 30 Jun 2020 00:44:16: #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 00:44:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:44:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:44:22: 21000000 INFO @ Tue, 30 Jun 2020 00:44:29: 22000000 INFO @ Tue, 30 Jun 2020 00:44:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:44:36: 23000000 INFO @ Tue, 30 Jun 2020 00:44:40: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:44:40: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:44:40: #1 total tags in treatment: 23580574 INFO @ Tue, 30 Jun 2020 00:44:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:44:40: #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 00:44:41: #1 tags after filtering in treatment: 23580574 INFO @ Tue, 30 Jun 2020 00:44:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:44:41: #1 finished! INFO @ Tue, 30 Jun 2020 00:44:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:44:42: #2 number of paired peaks: 249 WARNING @ Tue, 30 Jun 2020 00:44:42: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Tue, 30 Jun 2020 00:44:42: start model_add_line... INFO @ Tue, 30 Jun 2020 00:44:43: start X-correlation... INFO @ Tue, 30 Jun 2020 00:44:43: end of X-cor INFO @ Tue, 30 Jun 2020 00:44:43: #2 finished! INFO @ Tue, 30 Jun 2020 00:44:43: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 00:44:43: #2 alternative fragment length(s) may be 2,51 bps INFO @ Tue, 30 Jun 2020 00:44:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.20_model.r WARNING @ Tue, 30 Jun 2020 00:44:43: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:44:43: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Tue, 30 Jun 2020 00:44:43: #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 00:44:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:44:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:44:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:44:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:44:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.05_summits.bed INFO @ Tue, 30 Jun 2020 00:44:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3663 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:45:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:45:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:45:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:45:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.10_summits.bed INFO @ Tue, 30 Jun 2020 00:45:30: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (2549 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:45:32: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:45:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:45:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:45:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6811508/SRX6811508.20_summits.bed INFO @ Tue, 30 Jun 2020 00:45:56: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1295 records, 4 fields): 3 millis CompletedMACS2peakCalling