Job ID = 6527609 SRX = SRX1361352 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:45:51 prefetch.2.10.7: 1) Downloading 'SRR2749790'... 2020-06-29T12:45:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:50:18 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:50:18 prefetch.2.10.7: 1) 'SRR2749790' was downloaded successfully Read 30868255 spots for SRR2749790/SRR2749790.sra Written 30868255 spots for SRR2749790/SRR2749790.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: 00:14:34 30868255 reads; of these: 30868255 (100.00%) were unpaired; of these: 2260745 (7.32%) aligned 0 times 13381333 (43.35%) aligned exactly 1 time 15226177 (49.33%) aligned >1 times 92.68% overall alignment rate Time searching: 00:14:34 Overall time: 00:14:34 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] 7719231 / 28607510 = 0.2698 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 22:25:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.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 22:25:13: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:25:13: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:25:20: 1000000 INFO @ Mon, 29 Jun 2020 22:25:26: 2000000 INFO @ Mon, 29 Jun 2020 22:25:32: 3000000 INFO @ Mon, 29 Jun 2020 22:25:39: 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 22:25:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.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 22:25:43: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:25:43: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:25:45: 5000000 INFO @ Mon, 29 Jun 2020 22:25:50: 1000000 INFO @ Mon, 29 Jun 2020 22:25:52: 6000000 INFO @ Mon, 29 Jun 2020 22:25:57: 2000000 INFO @ Mon, 29 Jun 2020 22:25:58: 7000000 INFO @ Mon, 29 Jun 2020 22:26:03: 3000000 INFO @ Mon, 29 Jun 2020 22:26:05: 8000000 INFO @ Mon, 29 Jun 2020 22:26:10: 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 @ Mon, 29 Jun 2020 22:26:11: 9000000 INFO @ Mon, 29 Jun 2020 22:26:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.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 22:26:13: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:26:13: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:26:16: 5000000 INFO @ Mon, 29 Jun 2020 22:26:18: 10000000 INFO @ Mon, 29 Jun 2020 22:26:20: 1000000 INFO @ Mon, 29 Jun 2020 22:26:23: 6000000 INFO @ Mon, 29 Jun 2020 22:26:25: 11000000 INFO @ Mon, 29 Jun 2020 22:26:27: 2000000 INFO @ Mon, 29 Jun 2020 22:26:30: 7000000 INFO @ Mon, 29 Jun 2020 22:26:31: 12000000 INFO @ Mon, 29 Jun 2020 22:26:34: 3000000 INFO @ Mon, 29 Jun 2020 22:26:36: 8000000 INFO @ Mon, 29 Jun 2020 22:26:38: 13000000 INFO @ Mon, 29 Jun 2020 22:26:41: 4000000 INFO @ Mon, 29 Jun 2020 22:26:43: 9000000 INFO @ Mon, 29 Jun 2020 22:26:45: 14000000 INFO @ Mon, 29 Jun 2020 22:26:48: 5000000 INFO @ Mon, 29 Jun 2020 22:26:49: 10000000 INFO @ Mon, 29 Jun 2020 22:26:52: 15000000 INFO @ Mon, 29 Jun 2020 22:26:54: 6000000 INFO @ Mon, 29 Jun 2020 22:26:56: 11000000 INFO @ Mon, 29 Jun 2020 22:26:59: 16000000 INFO @ Mon, 29 Jun 2020 22:27:01: 7000000 INFO @ Mon, 29 Jun 2020 22:27:02: 12000000 INFO @ Mon, 29 Jun 2020 22:27:05: 17000000 INFO @ Mon, 29 Jun 2020 22:27:08: 8000000 INFO @ Mon, 29 Jun 2020 22:27:09: 13000000 INFO @ Mon, 29 Jun 2020 22:27:12: 18000000 INFO @ Mon, 29 Jun 2020 22:27:15: 9000000 INFO @ Mon, 29 Jun 2020 22:27:16: 14000000 INFO @ Mon, 29 Jun 2020 22:27:19: 19000000 INFO @ Mon, 29 Jun 2020 22:27:22: 10000000 INFO @ Mon, 29 Jun 2020 22:27:22: 15000000 INFO @ Mon, 29 Jun 2020 22:27:26: 20000000 INFO @ Mon, 29 Jun 2020 22:27:29: 11000000 INFO @ Mon, 29 Jun 2020 22:27:29: 16000000 INFO @ Mon, 29 Jun 2020 22:27:33: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:27:33: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:27:33: #1 total tags in treatment: 20888279 INFO @ Mon, 29 Jun 2020 22:27:33: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:27:33: #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 22:27:34: #1 tags after filtering in treatment: 20888279 INFO @ Mon, 29 Jun 2020 22:27:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:27:34: #1 finished! INFO @ Mon, 29 Jun 2020 22:27:34: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:27:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:27:35: #2 number of paired peaks: 478 WARNING @ Mon, 29 Jun 2020 22:27:35: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Mon, 29 Jun 2020 22:27:35: start model_add_line... INFO @ Mon, 29 Jun 2020 22:27:35: start X-correlation... INFO @ Mon, 29 Jun 2020 22:27:35: end of X-cor INFO @ Mon, 29 Jun 2020 22:27:35: #2 finished! INFO @ Mon, 29 Jun 2020 22:27:35: #2 predicted fragment length is 38 bps INFO @ Mon, 29 Jun 2020 22:27:35: #2 alternative fragment length(s) may be 3,38 bps INFO @ Mon, 29 Jun 2020 22:27:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.05_model.r WARNING @ Mon, 29 Jun 2020 22:27:35: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:27:35: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Mon, 29 Jun 2020 22:27:35: #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 22:27:35: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:27:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:27:35: 12000000 INFO @ Mon, 29 Jun 2020 22:27:36: 17000000 INFO @ Mon, 29 Jun 2020 22:27:42: 13000000 INFO @ Mon, 29 Jun 2020 22:27:43: 18000000 INFO @ Mon, 29 Jun 2020 22:27:49: 14000000 INFO @ Mon, 29 Jun 2020 22:27:49: 19000000 INFO @ Mon, 29 Jun 2020 22:27:55: 15000000 INFO @ Mon, 29 Jun 2020 22:27:57: 20000000 INFO @ Mon, 29 Jun 2020 22:28:02: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:28:03: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:28:03: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:28:03: #1 total tags in treatment: 20888279 INFO @ Mon, 29 Jun 2020 22:28:03: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:28:03: #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 22:28:03: #1 tags after filtering in treatment: 20888279 INFO @ Mon, 29 Jun 2020 22:28:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:28:03: #1 finished! INFO @ Mon, 29 Jun 2020 22:28:03: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:28:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:28:05: #2 number of paired peaks: 478 WARNING @ Mon, 29 Jun 2020 22:28:05: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Mon, 29 Jun 2020 22:28:05: start model_add_line... INFO @ Mon, 29 Jun 2020 22:28:05: start X-correlation... INFO @ Mon, 29 Jun 2020 22:28:05: end of X-cor INFO @ Mon, 29 Jun 2020 22:28:05: #2 finished! INFO @ Mon, 29 Jun 2020 22:28:05: #2 predicted fragment length is 38 bps INFO @ Mon, 29 Jun 2020 22:28:05: #2 alternative fragment length(s) may be 3,38 bps INFO @ Mon, 29 Jun 2020 22:28:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.10_model.r WARNING @ Mon, 29 Jun 2020 22:28:05: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:28:05: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Mon, 29 Jun 2020 22:28:05: #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 22:28:05: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:28:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:28:08: 17000000 INFO @ Mon, 29 Jun 2020 22:28:13: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:28:15: 18000000 INFO @ Mon, 29 Jun 2020 22:28:21: 19000000 INFO @ Mon, 29 Jun 2020 22:28:28: 20000000 INFO @ Mon, 29 Jun 2020 22:28:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:28:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:28:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.05_summits.bed INFO @ Mon, 29 Jun 2020 22:28:34: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9926 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:28:35: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:28:35: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:28:35: #1 total tags in treatment: 20888279 INFO @ Mon, 29 Jun 2020 22:28:35: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:28:35: #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 22:28:35: #1 tags after filtering in treatment: 20888279 INFO @ Mon, 29 Jun 2020 22:28:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:28:35: #1 finished! INFO @ Mon, 29 Jun 2020 22:28:35: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:28:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:28:37: #2 number of paired peaks: 478 WARNING @ Mon, 29 Jun 2020 22:28:37: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Mon, 29 Jun 2020 22:28:37: start model_add_line... INFO @ Mon, 29 Jun 2020 22:28:37: start X-correlation... INFO @ Mon, 29 Jun 2020 22:28:37: end of X-cor INFO @ Mon, 29 Jun 2020 22:28:37: #2 finished! INFO @ Mon, 29 Jun 2020 22:28:37: #2 predicted fragment length is 38 bps INFO @ Mon, 29 Jun 2020 22:28:37: #2 alternative fragment length(s) may be 3,38 bps INFO @ Mon, 29 Jun 2020 22:28:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.20_model.r WARNING @ Mon, 29 Jun 2020 22:28:37: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:28:37: #2 You may need to consider one of the other alternative d(s): 3,38 WARNING @ Mon, 29 Jun 2020 22:28:37: #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 22:28:37: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:28:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:28:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:29:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:29:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:29:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.10_summits.bed INFO @ Mon, 29 Jun 2020 22:29:01: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2463 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:29:14: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:29:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:29:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:29:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1361352/SRX1361352.20_summits.bed INFO @ Mon, 29 Jun 2020 22:29:35: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1141 records, 4 fields): 3 millis CompletedMACS2peakCalling