Job ID = 6455851 SRX = SRX3011255 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:14:51 prefetch.2.10.7: 1) Downloading 'SRR5834732'... 2020-06-21T10:14:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:18:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:18:33 prefetch.2.10.7: 1) 'SRR5834732' was downloaded successfully 2020-06-21T10:19:25 prefetch.2.10.7: 'SRR5834732' has 10 unresolved dependencies 2020-06-21T10:19:25 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:19:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:37 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:19:37 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:19:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:14 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:20:14 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:20:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:30 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:20:30 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:20:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:47 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:20:47 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:20:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:04 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:04 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:21:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:20 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:20 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:21:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:38 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:38 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:21:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:51 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:51 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:21:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:05 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:05 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:22:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:17 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 25387309 spots for SRR5834732/SRR5834732.sra Written 25387309 spots for SRR5834732/SRR5834732.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: 00:03:40 25387309 reads; of these: 25387309 (100.00%) were unpaired; of these: 312804 (1.23%) aligned 0 times 24551802 (96.71%) aligned exactly 1 time 522703 (2.06%) aligned >1 times 98.77% overall alignment rate Time searching: 00:03:40 Overall time: 00:03:40 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] 3628336 / 25074505 = 0.1447 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 19:33:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.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 19:33:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:32: 1000000 INFO @ Sun, 21 Jun 2020 19:33:38: 2000000 INFO @ Sun, 21 Jun 2020 19:33:44: 3000000 INFO @ Sun, 21 Jun 2020 19:33:49: 4000000 INFO @ Sun, 21 Jun 2020 19:33:55: 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 19:33:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.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 19:33:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:01: 6000000 INFO @ Sun, 21 Jun 2020 19:34:03: 1000000 INFO @ Sun, 21 Jun 2020 19:34:07: 7000000 INFO @ Sun, 21 Jun 2020 19:34:09: 2000000 INFO @ Sun, 21 Jun 2020 19:34:13: 8000000 INFO @ Sun, 21 Jun 2020 19:34:15: 3000000 INFO @ Sun, 21 Jun 2020 19:34:19: 9000000 INFO @ Sun, 21 Jun 2020 19:34:21: 4000000 INFO @ Sun, 21 Jun 2020 19:34:25: 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 19:34:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.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 19:34:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:27: 5000000 INFO @ Sun, 21 Jun 2020 19:34:31: 11000000 INFO @ Sun, 21 Jun 2020 19:34:33: 1000000 INFO @ Sun, 21 Jun 2020 19:34:33: 6000000 INFO @ Sun, 21 Jun 2020 19:34:37: 12000000 INFO @ Sun, 21 Jun 2020 19:34:39: 2000000 INFO @ Sun, 21 Jun 2020 19:34:39: 7000000 INFO @ Sun, 21 Jun 2020 19:34:43: 13000000 INFO @ Sun, 21 Jun 2020 19:34:45: 3000000 INFO @ Sun, 21 Jun 2020 19:34:46: 8000000 INFO @ Sun, 21 Jun 2020 19:34:49: 14000000 INFO @ Sun, 21 Jun 2020 19:34:52: 4000000 INFO @ Sun, 21 Jun 2020 19:34:52: 9000000 INFO @ Sun, 21 Jun 2020 19:34:55: 15000000 INFO @ Sun, 21 Jun 2020 19:34:58: 10000000 INFO @ Sun, 21 Jun 2020 19:34:58: 5000000 INFO @ Sun, 21 Jun 2020 19:35:02: 16000000 INFO @ Sun, 21 Jun 2020 19:35:04: 11000000 INFO @ Sun, 21 Jun 2020 19:35:04: 6000000 INFO @ Sun, 21 Jun 2020 19:35:08: 17000000 INFO @ Sun, 21 Jun 2020 19:35:10: 7000000 INFO @ Sun, 21 Jun 2020 19:35:10: 12000000 INFO @ Sun, 21 Jun 2020 19:35:14: 18000000 INFO @ Sun, 21 Jun 2020 19:35:16: 8000000 INFO @ Sun, 21 Jun 2020 19:35:16: 13000000 INFO @ Sun, 21 Jun 2020 19:35:20: 19000000 INFO @ Sun, 21 Jun 2020 19:35:22: 9000000 INFO @ Sun, 21 Jun 2020 19:35:22: 14000000 INFO @ Sun, 21 Jun 2020 19:35:26: 20000000 INFO @ Sun, 21 Jun 2020 19:35:28: 10000000 INFO @ Sun, 21 Jun 2020 19:35:29: 15000000 INFO @ Sun, 21 Jun 2020 19:35:32: 21000000 INFO @ Sun, 21 Jun 2020 19:35:35: 11000000 INFO @ Sun, 21 Jun 2020 19:35:35: 16000000 INFO @ Sun, 21 Jun 2020 19:35:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:35:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:35:35: #1 total tags in treatment: 21446169 INFO @ Sun, 21 Jun 2020 19:35:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:35: #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 19:35:36: #1 tags after filtering in treatment: 21445750 INFO @ Sun, 21 Jun 2020 19:35:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:37: #2 number of paired peaks: 173 WARNING @ Sun, 21 Jun 2020 19:35:37: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sun, 21 Jun 2020 19:35:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:37: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 19:35:37: #2 alternative fragment length(s) may be 4,185 bps INFO @ Sun, 21 Jun 2020 19:35:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.05_model.r INFO @ Sun, 21 Jun 2020 19:35:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:41: 12000000 INFO @ Sun, 21 Jun 2020 19:35:41: 17000000 INFO @ Sun, 21 Jun 2020 19:35:47: 13000000 INFO @ Sun, 21 Jun 2020 19:35:47: 18000000 INFO @ Sun, 21 Jun 2020 19:35:53: 14000000 INFO @ Sun, 21 Jun 2020 19:35:53: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:35:59: 15000000 INFO @ Sun, 21 Jun 2020 19:36:00: 20000000 INFO @ Sun, 21 Jun 2020 19:36:05: 16000000 INFO @ Sun, 21 Jun 2020 19:36:06: 21000000 INFO @ Sun, 21 Jun 2020 19:36:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:09: #1 total tags in treatment: 21446169 INFO @ Sun, 21 Jun 2020 19:36:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:09: #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 19:36:09: #1 tags after filtering in treatment: 21445750 INFO @ Sun, 21 Jun 2020 19:36:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:09: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:11: #2 number of paired peaks: 173 WARNING @ Sun, 21 Jun 2020 19:36:11: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sun, 21 Jun 2020 19:36:11: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:11: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:11: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:11: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:11: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 19:36:11: #2 alternative fragment length(s) may be 4,185 bps INFO @ Sun, 21 Jun 2020 19:36:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.10_model.r INFO @ Sun, 21 Jun 2020 19:36:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:11: 17000000 INFO @ Sun, 21 Jun 2020 19:36:17: 18000000 INFO @ Sun, 21 Jun 2020 19:36:24: 19000000 INFO @ Sun, 21 Jun 2020 19:36:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:29: 20000000 INFO @ Sun, 21 Jun 2020 19:36:35: 21000000 INFO @ Sun, 21 Jun 2020 19:36:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:38: #1 total tags in treatment: 21446169 INFO @ Sun, 21 Jun 2020 19:36:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:38: #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 19:36:38: #1 tags after filtering in treatment: 21445750 INFO @ Sun, 21 Jun 2020 19:36:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:40: #2 number of paired peaks: 173 WARNING @ Sun, 21 Jun 2020 19:36:40: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sun, 21 Jun 2020 19:36:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:40: #2 predicted fragment length is 185 bps INFO @ Sun, 21 Jun 2020 19:36:40: #2 alternative fragment length(s) may be 4,185 bps INFO @ Sun, 21 Jun 2020 19:36:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.20_model.r INFO @ Sun, 21 Jun 2020 19:36:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:36:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.05_summits.bed INFO @ Sun, 21 Jun 2020 19:36:48: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (7039 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:36:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.10_summits.bed INFO @ Sun, 21 Jun 2020 19:37:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2049 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:37:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011255/SRX3011255.20_summits.bed INFO @ Sun, 21 Jun 2020 19:37:51: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (229 records, 4 fields): 1 millis CompletedMACS2peakCalling