Job ID = 6527658 SRX = SRX193311 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:44:00 prefetch.2.10.7: 1) Downloading 'SRR585044'... 2020-06-29T13:44:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:49:05 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:49:05 prefetch.2.10.7: 1) 'SRR585044' was downloaded successfully Read 31198859 spots for SRR585044/SRR585044.sra Written 31198859 spots for SRR585044/SRR585044.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:19 31198859 reads; of these: 31198859 (100.00%) were unpaired; of these: 932027 (2.99%) aligned 0 times 19593741 (62.80%) aligned exactly 1 time 10673091 (34.21%) aligned >1 times 97.01% overall alignment rate Time searching: 00:12:19 Overall time: 00:12:19 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 16 files... [bam_rmdupse_core] 6170903 / 30266832 = 0.2039 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 @ Mon, 29 Jun 2020 23:18:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.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 @ Mon, 29 Jun 2020 23:18:04: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:18:04: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:18:10: 1000000 INFO @ Mon, 29 Jun 2020 23:18:16: 2000000 INFO @ Mon, 29 Jun 2020 23:18:22: 3000000 INFO @ Mon, 29 Jun 2020 23:18:28: 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 @ Mon, 29 Jun 2020 23:18:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.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 @ Mon, 29 Jun 2020 23:18:34: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:18:34: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:18:34: 5000000 INFO @ Mon, 29 Jun 2020 23:18:41: 1000000 INFO @ Mon, 29 Jun 2020 23:18:42: 6000000 INFO @ Mon, 29 Jun 2020 23:18:48: 2000000 INFO @ Mon, 29 Jun 2020 23:18:49: 7000000 INFO @ Mon, 29 Jun 2020 23:18:56: 3000000 INFO @ Mon, 29 Jun 2020 23:18:57: 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 @ Mon, 29 Jun 2020 23:19:03: 4000000 INFO @ Mon, 29 Jun 2020 23:19:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.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 @ Mon, 29 Jun 2020 23:19:04: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:19:04: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:19:04: 9000000 INFO @ Mon, 29 Jun 2020 23:19:11: 5000000 INFO @ Mon, 29 Jun 2020 23:19:11: 1000000 INFO @ Mon, 29 Jun 2020 23:19:12: 10000000 INFO @ Mon, 29 Jun 2020 23:19:18: 6000000 INFO @ Mon, 29 Jun 2020 23:19:19: 2000000 INFO @ Mon, 29 Jun 2020 23:19:19: 11000000 INFO @ Mon, 29 Jun 2020 23:19:25: 7000000 INFO @ Mon, 29 Jun 2020 23:19:26: 3000000 INFO @ Mon, 29 Jun 2020 23:19:27: 12000000 INFO @ Mon, 29 Jun 2020 23:19:33: 8000000 INFO @ Mon, 29 Jun 2020 23:19:34: 4000000 INFO @ Mon, 29 Jun 2020 23:19:34: 13000000 INFO @ Mon, 29 Jun 2020 23:19:40: 9000000 INFO @ Mon, 29 Jun 2020 23:19:41: 5000000 INFO @ Mon, 29 Jun 2020 23:19:41: 14000000 INFO @ Mon, 29 Jun 2020 23:19:47: 10000000 INFO @ Mon, 29 Jun 2020 23:19:48: 6000000 INFO @ Mon, 29 Jun 2020 23:19:48: 15000000 INFO @ Mon, 29 Jun 2020 23:19:55: 11000000 INFO @ Mon, 29 Jun 2020 23:19:55: 7000000 INFO @ Mon, 29 Jun 2020 23:19:56: 16000000 INFO @ Mon, 29 Jun 2020 23:20:02: 12000000 INFO @ Mon, 29 Jun 2020 23:20:02: 8000000 INFO @ Mon, 29 Jun 2020 23:20:03: 17000000 INFO @ Mon, 29 Jun 2020 23:20:09: 13000000 INFO @ Mon, 29 Jun 2020 23:20:09: 9000000 INFO @ Mon, 29 Jun 2020 23:20:10: 18000000 INFO @ Mon, 29 Jun 2020 23:20:16: 14000000 INFO @ Mon, 29 Jun 2020 23:20:17: 10000000 INFO @ Mon, 29 Jun 2020 23:20:17: 19000000 INFO @ Mon, 29 Jun 2020 23:20:23: 15000000 INFO @ Mon, 29 Jun 2020 23:20:24: 11000000 INFO @ Mon, 29 Jun 2020 23:20:24: 20000000 INFO @ Mon, 29 Jun 2020 23:20:30: 16000000 INFO @ Mon, 29 Jun 2020 23:20:31: 12000000 INFO @ Mon, 29 Jun 2020 23:20:31: 21000000 INFO @ Mon, 29 Jun 2020 23:20:37: 17000000 INFO @ Mon, 29 Jun 2020 23:20:38: 13000000 INFO @ Mon, 29 Jun 2020 23:20:39: 22000000 INFO @ Mon, 29 Jun 2020 23:20:44: 18000000 INFO @ Mon, 29 Jun 2020 23:20:45: 14000000 INFO @ Mon, 29 Jun 2020 23:20:46: 23000000 INFO @ Mon, 29 Jun 2020 23:20:52: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:20:52: 15000000 INFO @ Mon, 29 Jun 2020 23:20:53: 24000000 INFO @ Mon, 29 Jun 2020 23:20:54: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:20:54: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:20:54: #1 total tags in treatment: 24095929 INFO @ Mon, 29 Jun 2020 23:20:54: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:20:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:20:54: #1 tags after filtering in treatment: 24095929 INFO @ Mon, 29 Jun 2020 23:20:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:20:54: #1 finished! INFO @ Mon, 29 Jun 2020 23:20:54: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:20:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:20:56: #2 number of paired peaks: 417 WARNING @ Mon, 29 Jun 2020 23:20:56: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Mon, 29 Jun 2020 23:20:56: start model_add_line... INFO @ Mon, 29 Jun 2020 23:20:56: start X-correlation... INFO @ Mon, 29 Jun 2020 23:20:56: end of X-cor INFO @ Mon, 29 Jun 2020 23:20:56: #2 finished! INFO @ Mon, 29 Jun 2020 23:20:56: #2 predicted fragment length is 51 bps INFO @ Mon, 29 Jun 2020 23:20:56: #2 alternative fragment length(s) may be 2,51,538 bps INFO @ Mon, 29 Jun 2020 23:20:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.05_model.r WARNING @ Mon, 29 Jun 2020 23:20:56: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:20:56: #2 You may need to consider one of the other alternative d(s): 2,51,538 WARNING @ Mon, 29 Jun 2020 23:20:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:20:56: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:20:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:20:59: 20000000 INFO @ Mon, 29 Jun 2020 23:20:59: 16000000 INFO @ Mon, 29 Jun 2020 23:21:06: 21000000 INFO @ Mon, 29 Jun 2020 23:21:07: 17000000 INFO @ Mon, 29 Jun 2020 23:21:14: 22000000 INFO @ Mon, 29 Jun 2020 23:21:14: 18000000 INFO @ Mon, 29 Jun 2020 23:21:21: 23000000 INFO @ Mon, 29 Jun 2020 23:21:21: 19000000 INFO @ Mon, 29 Jun 2020 23:21:28: 24000000 INFO @ Mon, 29 Jun 2020 23:21:29: 20000000 INFO @ Mon, 29 Jun 2020 23:21:29: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:21:29: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:21:29: #1 total tags in treatment: 24095929 INFO @ Mon, 29 Jun 2020 23:21:29: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:21:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:21:29: #1 tags after filtering in treatment: 24095929 INFO @ Mon, 29 Jun 2020 23:21:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:21:29: #1 finished! INFO @ Mon, 29 Jun 2020 23:21:29: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:21:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:21:31: #2 number of paired peaks: 417 WARNING @ Mon, 29 Jun 2020 23:21:31: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Mon, 29 Jun 2020 23:21:31: start model_add_line... INFO @ Mon, 29 Jun 2020 23:21:31: start X-correlation... INFO @ Mon, 29 Jun 2020 23:21:31: end of X-cor INFO @ Mon, 29 Jun 2020 23:21:31: #2 finished! INFO @ Mon, 29 Jun 2020 23:21:31: #2 predicted fragment length is 51 bps INFO @ Mon, 29 Jun 2020 23:21:31: #2 alternative fragment length(s) may be 2,51,538 bps INFO @ Mon, 29 Jun 2020 23:21:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.10_model.r WARNING @ Mon, 29 Jun 2020 23:21:31: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:21:31: #2 You may need to consider one of the other alternative d(s): 2,51,538 WARNING @ Mon, 29 Jun 2020 23:21:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:21:31: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:21:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:21:35: 21000000 INFO @ Mon, 29 Jun 2020 23:21:40: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:21:41: 22000000 INFO @ Mon, 29 Jun 2020 23:21:47: 23000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:21:53: 24000000 INFO @ Mon, 29 Jun 2020 23:21:54: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:21:54: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:21:54: #1 total tags in treatment: 24095929 INFO @ Mon, 29 Jun 2020 23:21:54: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:21:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:21:54: #1 tags after filtering in treatment: 24095929 INFO @ Mon, 29 Jun 2020 23:21:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:21:54: #1 finished! INFO @ Mon, 29 Jun 2020 23:21:54: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:21:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:21:56: #2 number of paired peaks: 417 WARNING @ Mon, 29 Jun 2020 23:21:56: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Mon, 29 Jun 2020 23:21:56: start model_add_line... INFO @ Mon, 29 Jun 2020 23:21:56: start X-correlation... INFO @ Mon, 29 Jun 2020 23:21:56: end of X-cor INFO @ Mon, 29 Jun 2020 23:21:56: #2 finished! INFO @ Mon, 29 Jun 2020 23:21:56: #2 predicted fragment length is 51 bps INFO @ Mon, 29 Jun 2020 23:21:56: #2 alternative fragment length(s) may be 2,51,538 bps INFO @ Mon, 29 Jun 2020 23:21:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.20_model.r WARNING @ Mon, 29 Jun 2020 23:21:56: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:21:56: #2 You may need to consider one of the other alternative d(s): 2,51,538 WARNING @ Mon, 29 Jun 2020 23:21:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:21:56: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:21:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:22:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:22:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:22:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.05_summits.bed INFO @ Mon, 29 Jun 2020 23:22:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4024 records, 4 fields): 82 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:22:15: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:22:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:22:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:22:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.10_summits.bed INFO @ Mon, 29 Jun 2020 23:22:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2758 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:22:41: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:23:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:23:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:23:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193311/SRX193311.20_summits.bed INFO @ Mon, 29 Jun 2020 23:23:02: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1646 records, 4 fields): 3 millis CompletedMACS2peakCalling