Job ID = 6451809 SRX = ERX011423 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:26:04 prefetch.2.10.7: 1) Downloading 'ERR031144'... 2020-06-21T07:26:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:28:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:28:25 prefetch.2.10.7: 'ERR031144' is valid 2020-06-21T07:28:25 prefetch.2.10.7: 1) 'ERR031144' was downloaded successfully 2020-06-21T07:29:16 prefetch.2.10.7: 'ERR031144' has 10 unresolved dependencies 2020-06-21T07:29:16 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T07:29:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:29:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:29:33 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:29:33 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T07:29:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:29:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:29:51 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:29:51 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T07:29:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:30:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:30:03 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:30:03 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T07:30:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:30:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:30:22 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:30:22 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T07:30:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:30:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:30:41 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:30:41 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T07:30:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:30:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:30:57 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:30:57 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T07:30:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:31:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:31:11 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:31:11 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T07:31:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:31:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:31:25 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:31:25 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T07:31:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:31:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:31:37 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:31:37 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T07:31:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:31:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:31:53 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 26109729 spots for ERR031144/ERR031144.sra Written 26109729 spots for ERR031144/ERR031144.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:35 26109729 reads; of these: 26109729 (100.00%) were unpaired; of these: 1029291 (3.94%) aligned 0 times 19060191 (73.00%) aligned exactly 1 time 6020247 (23.06%) aligned >1 times 96.06% overall alignment rate Time searching: 00:05:36 Overall time: 00:05:36 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 8 files... [bam_rmdupse_core] 10794262 / 25080438 = 0.4304 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 16:43:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.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 16:43:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:43:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:43:30: 1000000 INFO @ Sun, 21 Jun 2020 16:43:36: 2000000 INFO @ Sun, 21 Jun 2020 16:43:42: 3000000 INFO @ Sun, 21 Jun 2020 16:43:48: 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 @ Sun, 21 Jun 2020 16:43:53: 5000000 INFO @ Sun, 21 Jun 2020 16:43:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.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 16:43:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:43:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:43:59: 6000000 INFO @ Sun, 21 Jun 2020 16:44:00: 1000000 INFO @ Sun, 21 Jun 2020 16:44:05: 7000000 INFO @ Sun, 21 Jun 2020 16:44:06: 2000000 INFO @ Sun, 21 Jun 2020 16:44:11: 8000000 INFO @ Sun, 21 Jun 2020 16:44:12: 3000000 INFO @ Sun, 21 Jun 2020 16:44:17: 9000000 INFO @ Sun, 21 Jun 2020 16:44:18: 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 @ Sun, 21 Jun 2020 16:44:23: 10000000 INFO @ Sun, 21 Jun 2020 16:44:24: 5000000 INFO @ Sun, 21 Jun 2020 16:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.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 16:44:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:44:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:44:29: 11000000 INFO @ Sun, 21 Jun 2020 16:44:30: 6000000 INFO @ Sun, 21 Jun 2020 16:44:31: 1000000 INFO @ Sun, 21 Jun 2020 16:44:36: 7000000 INFO @ Sun, 21 Jun 2020 16:44:36: 12000000 INFO @ Sun, 21 Jun 2020 16:44:37: 2000000 INFO @ Sun, 21 Jun 2020 16:44:42: 13000000 INFO @ Sun, 21 Jun 2020 16:44:42: 8000000 INFO @ Sun, 21 Jun 2020 16:44:43: 3000000 INFO @ Sun, 21 Jun 2020 16:44:48: 9000000 INFO @ Sun, 21 Jun 2020 16:44:48: 14000000 INFO @ Sun, 21 Jun 2020 16:44:49: 4000000 INFO @ Sun, 21 Jun 2020 16:44:50: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:44:50: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:44:50: #1 total tags in treatment: 14286176 INFO @ Sun, 21 Jun 2020 16:44:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:44:50: #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 16:44:51: #1 tags after filtering in treatment: 14286171 INFO @ Sun, 21 Jun 2020 16:44:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:44:51: #1 finished! INFO @ Sun, 21 Jun 2020 16:44:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:44:52: #2 number of paired peaks: 953 WARNING @ Sun, 21 Jun 2020 16:44:52: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Sun, 21 Jun 2020 16:44:52: start model_add_line... INFO @ Sun, 21 Jun 2020 16:44:52: start X-correlation... INFO @ Sun, 21 Jun 2020 16:44:52: end of X-cor INFO @ Sun, 21 Jun 2020 16:44:52: #2 finished! INFO @ Sun, 21 Jun 2020 16:44:52: #2 predicted fragment length is 164 bps INFO @ Sun, 21 Jun 2020 16:44:52: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 21 Jun 2020 16:44:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.05_model.r INFO @ Sun, 21 Jun 2020 16:44:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:44:54: 10000000 INFO @ Sun, 21 Jun 2020 16:44:55: 5000000 INFO @ Sun, 21 Jun 2020 16:45:00: 11000000 INFO @ Sun, 21 Jun 2020 16:45:01: 6000000 INFO @ Sun, 21 Jun 2020 16:45:07: 12000000 INFO @ Sun, 21 Jun 2020 16:45:07: 7000000 INFO @ Sun, 21 Jun 2020 16:45:13: 13000000 INFO @ Sun, 21 Jun 2020 16:45:13: 8000000 INFO @ Sun, 21 Jun 2020 16:45:19: 9000000 INFO @ Sun, 21 Jun 2020 16:45:19: 14000000 INFO @ Sun, 21 Jun 2020 16:45:21: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:45:21: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:45:21: #1 total tags in treatment: 14286176 INFO @ Sun, 21 Jun 2020 16:45:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:45:21: #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 16:45:22: #1 tags after filtering in treatment: 14286171 INFO @ Sun, 21 Jun 2020 16:45:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:45:22: #1 finished! INFO @ Sun, 21 Jun 2020 16:45:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:45:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:45:23: #2 number of paired peaks: 953 WARNING @ Sun, 21 Jun 2020 16:45:23: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Sun, 21 Jun 2020 16:45:23: start model_add_line... INFO @ Sun, 21 Jun 2020 16:45:23: start X-correlation... INFO @ Sun, 21 Jun 2020 16:45:23: end of X-cor INFO @ Sun, 21 Jun 2020 16:45:23: #2 finished! INFO @ Sun, 21 Jun 2020 16:45:23: #2 predicted fragment length is 164 bps INFO @ Sun, 21 Jun 2020 16:45:23: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 21 Jun 2020 16:45:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.10_model.r INFO @ Sun, 21 Jun 2020 16:45:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:45:24: 10000000 INFO @ Sun, 21 Jun 2020 16:45:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:45:29: 11000000 INFO @ Sun, 21 Jun 2020 16:45:35: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:45:40: 13000000 INFO @ Sun, 21 Jun 2020 16:45:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:45:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:45:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.05_summits.bed INFO @ Sun, 21 Jun 2020 16:45:43: Done! pass1 - making usageList (771 chroms): 2 millis pass2 - checking and writing primary data (5801 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:45:45: 14000000 INFO @ Sun, 21 Jun 2020 16:45:46: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:45:46: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:45:46: #1 total tags in treatment: 14286176 INFO @ Sun, 21 Jun 2020 16:45:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:45:46: #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 16:45:47: #1 tags after filtering in treatment: 14286171 INFO @ Sun, 21 Jun 2020 16:45:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:45:47: #1 finished! INFO @ Sun, 21 Jun 2020 16:45:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:45:48: #2 number of paired peaks: 953 WARNING @ Sun, 21 Jun 2020 16:45:48: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Sun, 21 Jun 2020 16:45:48: start model_add_line... INFO @ Sun, 21 Jun 2020 16:45:48: start X-correlation... INFO @ Sun, 21 Jun 2020 16:45:48: end of X-cor INFO @ Sun, 21 Jun 2020 16:45:48: #2 finished! INFO @ Sun, 21 Jun 2020 16:45:48: #2 predicted fragment length is 164 bps INFO @ Sun, 21 Jun 2020 16:45:48: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 21 Jun 2020 16:45:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.20_model.r INFO @ Sun, 21 Jun 2020 16:45:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:45:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:45:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:46:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:46:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:46:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.10_summits.bed INFO @ Sun, 21 Jun 2020 16:46:13: Done! pass1 - making usageList (631 chroms): 1 millis pass2 - checking and writing primary data (3706 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:46:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:46:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:46:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:46:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011423/ERX011423.20_summits.bed INFO @ Sun, 21 Jun 2020 16:46:38: Done! pass1 - making usageList (354 chroms): 1 millis pass2 - checking and writing primary data (1819 records, 4 fields): 13 millis CompletedMACS2peakCalling