Job ID = 6455133 SRX = SRX2779383 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:46:10 prefetch.2.10.7: 1) Downloading 'SRR5499064'... 2020-06-21T09:46:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:46:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:46:42 prefetch.2.10.7: 'SRR5499064' is valid 2020-06-21T09:46:42 prefetch.2.10.7: 1) 'SRR5499064' was downloaded successfully 2020-06-21T09:47:33 prefetch.2.10.7: 'SRR5499064' has 10 unresolved dependencies 2020-06-21T09:47:33 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T09:47:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:47:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:47:46 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:47:46 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T09:47:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:48:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:48:03 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:48:03 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T09:48:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:48:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:48:19 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:48:19 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T09:48:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:48:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:48:36 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:48:36 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T09:48:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:48:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:48:54 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:48:54 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T09:48:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:49:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:49:11 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:49:11 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T09:49:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:49:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:49:29 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:49:29 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T09:49:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:49:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:49:42 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:49:42 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T09:49:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:49:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:49:55 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T09:49:55 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T09:49:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:50:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:50:09 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 2506825 spots for SRR5499064/SRR5499064.sra Written 2506825 spots for SRR5499064/SRR5499064.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: 00:00:33 2506825 reads; of these: 2506825 (100.00%) were unpaired; of these: 61653 (2.46%) aligned 0 times 2378036 (94.86%) aligned exactly 1 time 67136 (2.68%) aligned >1 times 97.54% overall alignment rate Time searching: 00:00:33 Overall time: 00:00:33 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_rmdupse_core] 322059 / 2445172 = 0.1317 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 18:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.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 18:52:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:19: 1000000 INFO @ Sun, 21 Jun 2020 18:52:27: 2000000 INFO @ Sun, 21 Jun 2020 18:52:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:52:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:52:28: #1 total tags in treatment: 2123113 INFO @ Sun, 21 Jun 2020 18:52:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:28: #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 18:52:28: #1 tags after filtering in treatment: 2122573 INFO @ Sun, 21 Jun 2020 18:52:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:28: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:28: #2 number of paired peaks: 245 WARNING @ Sun, 21 Jun 2020 18:52:28: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Sun, 21 Jun 2020 18:52:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:28: #2 predicted fragment length is 107 bps INFO @ Sun, 21 Jun 2020 18:52:28: #2 alternative fragment length(s) may be 56,90,107,481,511,569 bps INFO @ Sun, 21 Jun 2020 18:52:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.05_model.r INFO @ Sun, 21 Jun 2020 18:52:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.05_summits.bed INFO @ Sun, 21 Jun 2020 18:52:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (46 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 18:52:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.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 18:52:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:48: 1000000 INFO @ Sun, 21 Jun 2020 18:52:55: 2000000 INFO @ Sun, 21 Jun 2020 18:52:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:52:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:52:56: #1 total tags in treatment: 2123113 INFO @ Sun, 21 Jun 2020 18:52:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:56: #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 18:52:56: #1 tags after filtering in treatment: 2122573 INFO @ Sun, 21 Jun 2020 18:52:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:56: #2 number of paired peaks: 245 WARNING @ Sun, 21 Jun 2020 18:52:56: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Sun, 21 Jun 2020 18:52:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:56: #2 predicted fragment length is 107 bps INFO @ Sun, 21 Jun 2020 18:52:56: #2 alternative fragment length(s) may be 56,90,107,481,511,569 bps INFO @ Sun, 21 Jun 2020 18:52:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.10_model.r INFO @ Sun, 21 Jun 2020 18:52:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.10_summits.bed INFO @ Sun, 21 Jun 2020 18:53:03: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 18:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.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 18:53:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:53:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:53:18: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:53:25: 2000000 INFO @ Sun, 21 Jun 2020 18:53:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:53:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:53:26: #1 total tags in treatment: 2123113 INFO @ Sun, 21 Jun 2020 18:53:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:26: #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 18:53:26: #1 tags after filtering in treatment: 2122573 INFO @ Sun, 21 Jun 2020 18:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:26: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:26: #2 number of paired peaks: 245 WARNING @ Sun, 21 Jun 2020 18:53:26: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Sun, 21 Jun 2020 18:53:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:26: #2 predicted fragment length is 107 bps INFO @ Sun, 21 Jun 2020 18:53:26: #2 alternative fragment length(s) may be 56,90,107,481,511,569 bps INFO @ Sun, 21 Jun 2020 18:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.20_model.r INFO @ Sun, 21 Jun 2020 18:53:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:53:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2779383/SRX2779383.20_summits.bed INFO @ Sun, 21 Jun 2020 18:53:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 7 millis CompletedMACS2peakCalling