Job ID = 6453878 SRX = SRX1550612 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:54:50 prefetch.2.10.7: 1) Downloading 'SRR3130862'... 2020-06-21T08:54:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:57:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:57:01 prefetch.2.10.7: 'SRR3130862' is valid 2020-06-21T08:57:01 prefetch.2.10.7: 1) 'SRR3130862' was downloaded successfully Read 4000000 spots for SRR3130862/SRR3130862.sra Written 4000000 spots for SRR3130862/SRR3130862.sra 2020-06-21T08:57:23 prefetch.2.10.7: 1) Downloading 'SRR3130863'... 2020-06-21T08:57:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:58:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:58:07 prefetch.2.10.7: 'SRR3130863' is valid 2020-06-21T08:58:07 prefetch.2.10.7: 1) 'SRR3130863' was downloaded successfully Read 4000000 spots for SRR3130863/SRR3130863.sra Written 4000000 spots for SRR3130863/SRR3130863.sra 2020-06-21T08:58:29 prefetch.2.10.7: 1) Downloading 'SRR3130864'... 2020-06-21T08:58:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:59:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:59:22 prefetch.2.10.7: 'SRR3130864' is valid 2020-06-21T08:59:22 prefetch.2.10.7: 1) 'SRR3130864' was downloaded successfully Read 4000000 spots for SRR3130864/SRR3130864.sra Written 4000000 spots for SRR3130864/SRR3130864.sra 2020-06-21T08:59:47 prefetch.2.10.7: 1) Downloading 'SRR3130865'... 2020-06-21T08:59:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:00:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:00:23 prefetch.2.10.7: 'SRR3130865' is valid 2020-06-21T09:00:23 prefetch.2.10.7: 1) 'SRR3130865' was downloaded successfully Read 4000000 spots for SRR3130865/SRR3130865.sra Written 4000000 spots for SRR3130865/SRR3130865.sra 2020-06-21T09:00:45 prefetch.2.10.7: 1) Downloading 'SRR3130866'... 2020-06-21T09:00:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:01:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:01:31 prefetch.2.10.7: 'SRR3130866' is valid 2020-06-21T09:01:31 prefetch.2.10.7: 1) 'SRR3130866' was downloaded successfully Read 4000000 spots for SRR3130866/SRR3130866.sra Written 4000000 spots for SRR3130866/SRR3130866.sra 2020-06-21T09:01:54 prefetch.2.10.7: 1) Downloading 'SRR3130867'... 2020-06-21T09:01:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:03:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:03:29 prefetch.2.10.7: 'SRR3130867' is valid 2020-06-21T09:03:29 prefetch.2.10.7: 1) 'SRR3130867' was downloaded successfully Read 4000000 spots for SRR3130867/SRR3130867.sra Written 4000000 spots for SRR3130867/SRR3130867.sra 2020-06-21T09:03:51 prefetch.2.10.7: 1) Downloading 'SRR3130868'... 2020-06-21T09:03:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:04:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:04:28 prefetch.2.10.7: 'SRR3130868' is valid 2020-06-21T09:04:28 prefetch.2.10.7: 1) 'SRR3130868' was downloaded successfully Read 1726636 spots for SRR3130868/SRR3130868.sra Written 1726636 spots for SRR3130868/SRR3130868.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: 00:06:31 25726636 reads; of these: 25726636 (100.00%) were unpaired; of these: 2305502 (8.96%) aligned 0 times 17956532 (69.80%) aligned exactly 1 time 5464602 (21.24%) aligned >1 times 91.04% overall alignment rate Time searching: 00:06:31 Overall time: 00:06:31 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] 4308173 / 23421134 = 0.1839 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 @ Sun, 21 Jun 2020 18:17:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.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 @ Sun, 21 Jun 2020 18:17:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:30: 1000000 INFO @ Sun, 21 Jun 2020 18:17:35: 2000000 INFO @ Sun, 21 Jun 2020 18:17:41: 3000000 INFO @ Sun, 21 Jun 2020 18:17:46: 4000000 INFO @ Sun, 21 Jun 2020 18:17:51: 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 @ Sun, 21 Jun 2020 18:17:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.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 @ Sun, 21 Jun 2020 18:17:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:57: 6000000 INFO @ Sun, 21 Jun 2020 18:18:01: 1000000 INFO @ Sun, 21 Jun 2020 18:18:03: 7000000 INFO @ Sun, 21 Jun 2020 18:18:07: 2000000 INFO @ Sun, 21 Jun 2020 18:18:09: 8000000 INFO @ Sun, 21 Jun 2020 18:18:14: 3000000 INFO @ Sun, 21 Jun 2020 18:18:15: 9000000 INFO @ Sun, 21 Jun 2020 18:18:21: 4000000 INFO @ Sun, 21 Jun 2020 18:18:21: 10000000 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 @ Sun, 21 Jun 2020 18:18:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.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 @ Sun, 21 Jun 2020 18:18:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:27: 11000000 INFO @ Sun, 21 Jun 2020 18:18:28: 5000000 INFO @ Sun, 21 Jun 2020 18:18:31: 1000000 INFO @ Sun, 21 Jun 2020 18:18:33: 12000000 INFO @ Sun, 21 Jun 2020 18:18:35: 6000000 INFO @ Sun, 21 Jun 2020 18:18:38: 2000000 INFO @ Sun, 21 Jun 2020 18:18:39: 13000000 INFO @ Sun, 21 Jun 2020 18:18:41: 7000000 INFO @ Sun, 21 Jun 2020 18:18:44: 3000000 INFO @ Sun, 21 Jun 2020 18:18:45: 14000000 INFO @ Sun, 21 Jun 2020 18:18:48: 8000000 INFO @ Sun, 21 Jun 2020 18:18:51: 15000000 INFO @ Sun, 21 Jun 2020 18:18:51: 4000000 INFO @ Sun, 21 Jun 2020 18:18:55: 9000000 INFO @ Sun, 21 Jun 2020 18:18:57: 16000000 INFO @ Sun, 21 Jun 2020 18:18:58: 5000000 INFO @ Sun, 21 Jun 2020 18:19:02: 10000000 INFO @ Sun, 21 Jun 2020 18:19:04: 17000000 INFO @ Sun, 21 Jun 2020 18:19:05: 6000000 INFO @ Sun, 21 Jun 2020 18:19:09: 11000000 INFO @ Sun, 21 Jun 2020 18:19:11: 18000000 INFO @ Sun, 21 Jun 2020 18:19:12: 7000000 INFO @ Sun, 21 Jun 2020 18:19:16: 12000000 INFO @ Sun, 21 Jun 2020 18:19:17: 19000000 INFO @ Sun, 21 Jun 2020 18:19:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:19:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:19:18: #1 total tags in treatment: 19112961 INFO @ Sun, 21 Jun 2020 18:19:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:19:18: 8000000 INFO @ Sun, 21 Jun 2020 18:19:19: #1 tags after filtering in treatment: 19112961 INFO @ Sun, 21 Jun 2020 18:19:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:19: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:19:20: #2 number of paired peaks: 663 WARNING @ Sun, 21 Jun 2020 18:19:20: Fewer paired peaks (663) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 663 pairs to build model! INFO @ Sun, 21 Jun 2020 18:19:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:19:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:19:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:19:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:19:20: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 18:19:20: #2 alternative fragment length(s) may be 71 bps INFO @ Sun, 21 Jun 2020 18:19:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.05_model.r WARNING @ Sun, 21 Jun 2020 18:19:20: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:19:20: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sun, 21 Jun 2020 18:19:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:19:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:19:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:19:23: 13000000 INFO @ Sun, 21 Jun 2020 18:19:25: 9000000 INFO @ Sun, 21 Jun 2020 18:19:29: 14000000 INFO @ Sun, 21 Jun 2020 18:19:32: 10000000 INFO @ Sun, 21 Jun 2020 18:19:36: 15000000 INFO @ Sun, 21 Jun 2020 18:19:39: 11000000 INFO @ Sun, 21 Jun 2020 18:19:43: 16000000 INFO @ Sun, 21 Jun 2020 18:19:46: 12000000 INFO @ Sun, 21 Jun 2020 18:19:50: 17000000 INFO @ Sun, 21 Jun 2020 18:19:52: 13000000 INFO @ Sun, 21 Jun 2020 18:19:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:19:57: 18000000 INFO @ Sun, 21 Jun 2020 18:19:59: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:20:03: 19000000 INFO @ Sun, 21 Jun 2020 18:20:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:20:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:20:04: #1 total tags in treatment: 19112961 INFO @ Sun, 21 Jun 2020 18:20:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:20:05: #1 tags after filtering in treatment: 19112961 INFO @ Sun, 21 Jun 2020 18:20:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:06: 15000000 INFO @ Sun, 21 Jun 2020 18:20:06: #2 number of paired peaks: 663 WARNING @ Sun, 21 Jun 2020 18:20:06: Fewer paired peaks (663) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 663 pairs to build model! INFO @ Sun, 21 Jun 2020 18:20:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:06: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 18:20:06: #2 alternative fragment length(s) may be 71 bps INFO @ Sun, 21 Jun 2020 18:20:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.10_model.r WARNING @ Sun, 21 Jun 2020 18:20:06: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:06: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sun, 21 Jun 2020 18:20:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:20:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:13: 16000000 INFO @ Sun, 21 Jun 2020 18:20:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.05_summits.bed INFO @ Sun, 21 Jun 2020 18:20:13: Done! pass1 - making usageList (609 chroms): 1 millis pass2 - checking and writing primary data (4415 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:20:19: 17000000 INFO @ Sun, 21 Jun 2020 18:20:25: 18000000 INFO @ Sun, 21 Jun 2020 18:20:32: 19000000 INFO @ Sun, 21 Jun 2020 18:20:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:20:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:20:33: #1 total tags in treatment: 19112961 INFO @ Sun, 21 Jun 2020 18:20:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:20:33: #1 tags after filtering in treatment: 19112961 INFO @ Sun, 21 Jun 2020 18:20:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:33: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:34: #2 number of paired peaks: 663 WARNING @ Sun, 21 Jun 2020 18:20:34: Fewer paired peaks (663) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 663 pairs to build model! INFO @ Sun, 21 Jun 2020 18:20:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:34: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:34: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:34: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:34: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 18:20:34: #2 alternative fragment length(s) may be 71 bps INFO @ Sun, 21 Jun 2020 18:20:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.20_model.r WARNING @ Sun, 21 Jun 2020 18:20:35: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:35: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sun, 21 Jun 2020 18:20:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:20:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:20:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.10_summits.bed INFO @ Sun, 21 Jun 2020 18:20:59: Done! pass1 - making usageList (506 chroms): 1 millis pass2 - checking and writing primary data (2636 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550612/SRX1550612.20_summits.bed INFO @ Sun, 21 Jun 2020 18:21:27: Done! pass1 - making usageList (440 chroms): 1 millis pass2 - checking and writing primary data (1865 records, 4 fields): 14 millis CompletedMACS2peakCalling