Job ID = 6455854 SRX = SRX3011258 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:46:38 prefetch.2.10.7: 1) Downloading 'SRR5834735'... 2020-06-21T10:46:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:50:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:50:26 prefetch.2.10.7: 'SRR5834735' is valid 2020-06-21T10:50:26 prefetch.2.10.7: 1) 'SRR5834735' was downloaded successfully 2020-06-21T10:51:18 prefetch.2.10.7: 'SRR5834735' has 10 unresolved dependencies 2020-06-21T10:51:18 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:51:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:51:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:51:30 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:51:30 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:51:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:51:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:51:47 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:51:47 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:51:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:52:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:52:01 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:52:01 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:52:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:52:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:52:18 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:52:18 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:52:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:52:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:52:35 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:52:35 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:52:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:52:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:52:51 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:52:51 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:52:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:53:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:53:08 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:53:08 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:53:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:53:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:53:22 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:53:22 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:53:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:53:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:53:36 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:53:36 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:53:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:53:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:53:49 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 22641356 spots for SRR5834735/SRR5834735.sra Written 22641356 spots for SRR5834735/SRR5834735.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: 00:03:23 22641356 reads; of these: 22641356 (100.00%) were unpaired; of these: 295753 (1.31%) aligned 0 times 21789177 (96.24%) aligned exactly 1 time 556426 (2.46%) aligned >1 times 98.69% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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] 2661728 / 22345603 = 0.1191 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 20:04:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.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 20:04:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:04:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:04:06: 1000000 INFO @ Sun, 21 Jun 2020 20:04:11: 2000000 INFO @ Sun, 21 Jun 2020 20:04:16: 3000000 INFO @ Sun, 21 Jun 2020 20:04:20: 4000000 INFO @ Sun, 21 Jun 2020 20:04:25: 5000000 INFO @ Sun, 21 Jun 2020 20:04:30: 6000000 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 20:04:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.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 20:04:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:04:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:04:34: 7000000 INFO @ Sun, 21 Jun 2020 20:04:37: 1000000 INFO @ Sun, 21 Jun 2020 20:04:39: 8000000 INFO @ Sun, 21 Jun 2020 20:04:41: 2000000 INFO @ Sun, 21 Jun 2020 20:04:44: 9000000 INFO @ Sun, 21 Jun 2020 20:04:46: 3000000 INFO @ Sun, 21 Jun 2020 20:04:49: 10000000 INFO @ Sun, 21 Jun 2020 20:04:51: 4000000 INFO @ Sun, 21 Jun 2020 20:04:54: 11000000 INFO @ Sun, 21 Jun 2020 20:04:56: 5000000 INFO @ Sun, 21 Jun 2020 20:04:59: 12000000 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 20:05:01: 6000000 INFO @ Sun, 21 Jun 2020 20:05:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.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 20:05:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:05:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:05:04: 13000000 INFO @ Sun, 21 Jun 2020 20:05:06: 7000000 INFO @ Sun, 21 Jun 2020 20:05:07: 1000000 INFO @ Sun, 21 Jun 2020 20:05:09: 14000000 INFO @ Sun, 21 Jun 2020 20:05:11: 8000000 INFO @ Sun, 21 Jun 2020 20:05:12: 2000000 INFO @ Sun, 21 Jun 2020 20:05:14: 15000000 INFO @ Sun, 21 Jun 2020 20:05:16: 9000000 INFO @ Sun, 21 Jun 2020 20:05:17: 3000000 INFO @ Sun, 21 Jun 2020 20:05:19: 16000000 INFO @ Sun, 21 Jun 2020 20:05:21: 10000000 INFO @ Sun, 21 Jun 2020 20:05:22: 4000000 INFO @ Sun, 21 Jun 2020 20:05:24: 17000000 INFO @ Sun, 21 Jun 2020 20:05:26: 11000000 INFO @ Sun, 21 Jun 2020 20:05:27: 5000000 INFO @ Sun, 21 Jun 2020 20:05:29: 18000000 INFO @ Sun, 21 Jun 2020 20:05:31: 12000000 INFO @ Sun, 21 Jun 2020 20:05:32: 6000000 INFO @ Sun, 21 Jun 2020 20:05:34: 19000000 INFO @ Sun, 21 Jun 2020 20:05:36: 13000000 INFO @ Sun, 21 Jun 2020 20:05:37: 7000000 INFO @ Sun, 21 Jun 2020 20:05:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:05:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:05:37: #1 total tags in treatment: 19683875 INFO @ Sun, 21 Jun 2020 20:05:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:05:37: #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 20:05:38: #1 tags after filtering in treatment: 19683511 INFO @ Sun, 21 Jun 2020 20:05:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:05:38: #1 finished! INFO @ Sun, 21 Jun 2020 20:05:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:05:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:05:39: #2 number of paired peaks: 119 WARNING @ Sun, 21 Jun 2020 20:05:39: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sun, 21 Jun 2020 20:05:39: start model_add_line... INFO @ Sun, 21 Jun 2020 20:05:39: start X-correlation... INFO @ Sun, 21 Jun 2020 20:05:39: end of X-cor INFO @ Sun, 21 Jun 2020 20:05:39: #2 finished! INFO @ Sun, 21 Jun 2020 20:05:39: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 20:05:39: #2 alternative fragment length(s) may be 3,90,138,156 bps INFO @ Sun, 21 Jun 2020 20:05:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.05_model.r INFO @ Sun, 21 Jun 2020 20:05:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:05:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:05:41: 14000000 INFO @ Sun, 21 Jun 2020 20:05:42: 8000000 INFO @ Sun, 21 Jun 2020 20:05:46: 15000000 INFO @ Sun, 21 Jun 2020 20:05:47: 9000000 INFO @ Sun, 21 Jun 2020 20:05:51: 16000000 INFO @ Sun, 21 Jun 2020 20:05:52: 10000000 INFO @ Sun, 21 Jun 2020 20:05:56: 17000000 INFO @ Sun, 21 Jun 2020 20:05:56: 11000000 INFO @ Sun, 21 Jun 2020 20:06:01: 18000000 INFO @ Sun, 21 Jun 2020 20:06:02: 12000000 INFO @ Sun, 21 Jun 2020 20:06:06: 19000000 INFO @ Sun, 21 Jun 2020 20:06:06: 13000000 INFO @ Sun, 21 Jun 2020 20:06:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:06:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:06:09: #1 total tags in treatment: 19683875 INFO @ Sun, 21 Jun 2020 20:06:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:06:09: #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 20:06:10: #1 tags after filtering in treatment: 19683511 INFO @ Sun, 21 Jun 2020 20:06:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:06:10: #1 finished! INFO @ Sun, 21 Jun 2020 20:06:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:06:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:06:11: #2 number of paired peaks: 119 WARNING @ Sun, 21 Jun 2020 20:06:11: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sun, 21 Jun 2020 20:06:11: start model_add_line... INFO @ Sun, 21 Jun 2020 20:06:11: start X-correlation... INFO @ Sun, 21 Jun 2020 20:06:11: end of X-cor INFO @ Sun, 21 Jun 2020 20:06:11: #2 finished! INFO @ Sun, 21 Jun 2020 20:06:11: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 20:06:11: #2 alternative fragment length(s) may be 3,90,138,156 bps INFO @ Sun, 21 Jun 2020 20:06:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.10_model.r INFO @ Sun, 21 Jun 2020 20:06:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:06:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:06:11: 14000000 INFO @ Sun, 21 Jun 2020 20:06:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:06:16: 15000000 INFO @ Sun, 21 Jun 2020 20:06:21: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:06:26: 17000000 INFO @ Sun, 21 Jun 2020 20:06:31: 18000000 INFO @ Sun, 21 Jun 2020 20:06:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:06:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:06:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.05_summits.bed INFO @ Sun, 21 Jun 2020 20:06:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1750 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:06:36: 19000000 INFO @ Sun, 21 Jun 2020 20:06:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:06:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:06:39: #1 total tags in treatment: 19683875 INFO @ Sun, 21 Jun 2020 20:06:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:06:39: #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 20:06:40: #1 tags after filtering in treatment: 19683511 INFO @ Sun, 21 Jun 2020 20:06:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:06:40: #1 finished! INFO @ Sun, 21 Jun 2020 20:06:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:06:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:06:41: #2 number of paired peaks: 119 WARNING @ Sun, 21 Jun 2020 20:06:41: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sun, 21 Jun 2020 20:06:41: start model_add_line... INFO @ Sun, 21 Jun 2020 20:06:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:06:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:06:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:06:41: #2 predicted fragment length is 138 bps INFO @ Sun, 21 Jun 2020 20:06:41: #2 alternative fragment length(s) may be 3,90,138,156 bps INFO @ Sun, 21 Jun 2020 20:06:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.20_model.r INFO @ Sun, 21 Jun 2020 20:06:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:06:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:06:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:07:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:07:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.10_summits.bed INFO @ Sun, 21 Jun 2020 20:07:07: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (186 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:07:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:07:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:07:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011258/SRX3011258.20_summits.bed INFO @ Sun, 21 Jun 2020 20:07:40: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 1 millis CompletedMACS2peakCalling