Job ID = 6497871 SRX = SRX2068662 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:41:39 prefetch.2.10.7: 1) Downloading 'SRR4101018'... 2020-06-25T22:41:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:45:57 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:45:57 prefetch.2.10.7: 1) 'SRR4101018' was downloaded successfully 2020-06-25T22:46:48 prefetch.2.10.7: 'SRR4101018' has 10 unresolved dependencies 2020-06-25T22:46:48 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-25T22:46:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:47:07 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:47:07 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:47:07 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-25T22:47:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:47:40 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:47:40 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:47:40 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-25T22:47:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:49:17 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:49:17 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:49:17 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-25T22:49:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:49:31 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:49:31 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:49:31 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-25T22:49:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:49:47 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:49:47 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:49:47 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-25T22:49:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:50:03 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:50:04 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:50:04 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-25T22:50:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:50:16 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:50:16 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:50:16 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-25T22:50:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:50:30 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:50:30 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:50:30 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-25T22:50:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:50:39 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:50:39 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:50:39 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-25T22:50:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:50:53 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:50:53 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 47610776 spots for SRR4101018/SRR4101018.sra Written 47610776 spots for SRR4101018/SRR4101018.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: 00:08:08 47610776 reads; of these: 47610776 (100.00%) were unpaired; of these: 14758622 (31.00%) aligned 0 times 25427959 (53.41%) aligned exactly 1 time 7424195 (15.59%) aligned >1 times 69.00% overall alignment rate Time searching: 00:08:08 Overall time: 00:08:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 8817696 / 32852154 = 0.2684 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 @ Fri, 26 Jun 2020 08:11:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.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 @ Fri, 26 Jun 2020 08:11:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:11:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:11:49: 1000000 INFO @ Fri, 26 Jun 2020 08:11:55: 2000000 INFO @ Fri, 26 Jun 2020 08:12:00: 3000000 INFO @ Fri, 26 Jun 2020 08:12:06: 4000000 INFO @ Fri, 26 Jun 2020 08:12:11: 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 @ Fri, 26 Jun 2020 08:12:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.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 @ Fri, 26 Jun 2020 08:12:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:12:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:12:16: 6000000 INFO @ Fri, 26 Jun 2020 08:12:19: 1000000 INFO @ Fri, 26 Jun 2020 08:12:22: 7000000 INFO @ Fri, 26 Jun 2020 08:12:25: 2000000 INFO @ Fri, 26 Jun 2020 08:12:28: 8000000 INFO @ Fri, 26 Jun 2020 08:12:31: 3000000 INFO @ Fri, 26 Jun 2020 08:12:33: 9000000 INFO @ Fri, 26 Jun 2020 08:12:37: 4000000 INFO @ Fri, 26 Jun 2020 08:12:39: 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 @ Fri, 26 Jun 2020 08:12:43: 5000000 INFO @ Fri, 26 Jun 2020 08:12:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.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 @ Fri, 26 Jun 2020 08:12:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:12:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:12:45: 11000000 INFO @ Fri, 26 Jun 2020 08:12:49: 6000000 INFO @ Fri, 26 Jun 2020 08:12:50: 1000000 INFO @ Fri, 26 Jun 2020 08:12:51: 12000000 INFO @ Fri, 26 Jun 2020 08:12:56: 7000000 INFO @ Fri, 26 Jun 2020 08:12:56: 2000000 INFO @ Fri, 26 Jun 2020 08:12:58: 13000000 INFO @ Fri, 26 Jun 2020 08:13:02: 8000000 INFO @ Fri, 26 Jun 2020 08:13:03: 3000000 INFO @ Fri, 26 Jun 2020 08:13:04: 14000000 INFO @ Fri, 26 Jun 2020 08:13:08: 9000000 INFO @ Fri, 26 Jun 2020 08:13:09: 4000000 INFO @ Fri, 26 Jun 2020 08:13:10: 15000000 INFO @ Fri, 26 Jun 2020 08:13:15: 10000000 INFO @ Fri, 26 Jun 2020 08:13:15: 5000000 INFO @ Fri, 26 Jun 2020 08:13:17: 16000000 INFO @ Fri, 26 Jun 2020 08:13:21: 11000000 INFO @ Fri, 26 Jun 2020 08:13:21: 6000000 INFO @ Fri, 26 Jun 2020 08:13:23: 17000000 INFO @ Fri, 26 Jun 2020 08:13:28: 7000000 INFO @ Fri, 26 Jun 2020 08:13:28: 12000000 INFO @ Fri, 26 Jun 2020 08:13:30: 18000000 INFO @ Fri, 26 Jun 2020 08:13:34: 8000000 INFO @ Fri, 26 Jun 2020 08:13:34: 13000000 INFO @ Fri, 26 Jun 2020 08:13:36: 19000000 INFO @ Fri, 26 Jun 2020 08:13:40: 9000000 INFO @ Fri, 26 Jun 2020 08:13:41: 14000000 INFO @ Fri, 26 Jun 2020 08:13:43: 20000000 INFO @ Fri, 26 Jun 2020 08:13:46: 10000000 INFO @ Fri, 26 Jun 2020 08:13:47: 15000000 INFO @ Fri, 26 Jun 2020 08:13:49: 21000000 INFO @ Fri, 26 Jun 2020 08:13:53: 11000000 INFO @ Fri, 26 Jun 2020 08:13:54: 16000000 INFO @ Fri, 26 Jun 2020 08:13:55: 22000000 INFO @ Fri, 26 Jun 2020 08:13:59: 12000000 INFO @ Fri, 26 Jun 2020 08:14:01: 17000000 INFO @ Fri, 26 Jun 2020 08:14:02: 23000000 INFO @ Fri, 26 Jun 2020 08:14:05: 13000000 INFO @ Fri, 26 Jun 2020 08:14:07: 18000000 INFO @ Fri, 26 Jun 2020 08:14:08: 24000000 INFO @ Fri, 26 Jun 2020 08:14:08: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:14:08: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:14:08: #1 total tags in treatment: 24034458 INFO @ Fri, 26 Jun 2020 08:14:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:14:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:14:09: #1 tags after filtering in treatment: 24034458 INFO @ Fri, 26 Jun 2020 08:14:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:14:09: #1 finished! INFO @ Fri, 26 Jun 2020 08:14:09: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:14:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:14:10: #2 number of paired peaks: 154 WARNING @ Fri, 26 Jun 2020 08:14:10: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 26 Jun 2020 08:14:10: start model_add_line... INFO @ Fri, 26 Jun 2020 08:14:11: start X-correlation... INFO @ Fri, 26 Jun 2020 08:14:11: end of X-cor INFO @ Fri, 26 Jun 2020 08:14:11: #2 finished! INFO @ Fri, 26 Jun 2020 08:14:11: #2 predicted fragment length is 145 bps INFO @ Fri, 26 Jun 2020 08:14:11: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 26 Jun 2020 08:14:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.05_model.r INFO @ Fri, 26 Jun 2020 08:14:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:14:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:14:11: 14000000 INFO @ Fri, 26 Jun 2020 08:14:13: 19000000 INFO @ Fri, 26 Jun 2020 08:14:17: 15000000 INFO @ Fri, 26 Jun 2020 08:14:19: 20000000 INFO @ Fri, 26 Jun 2020 08:14:23: 16000000 INFO @ Fri, 26 Jun 2020 08:14:25: 21000000 INFO @ Fri, 26 Jun 2020 08:14:28: 17000000 INFO @ Fri, 26 Jun 2020 08:14:31: 22000000 INFO @ Fri, 26 Jun 2020 08:14:34: 18000000 INFO @ Fri, 26 Jun 2020 08:14:37: 23000000 INFO @ Fri, 26 Jun 2020 08:14:40: 19000000 INFO @ Fri, 26 Jun 2020 08:14:43: 24000000 INFO @ Fri, 26 Jun 2020 08:14:43: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:14:43: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:14:43: #1 total tags in treatment: 24034458 INFO @ Fri, 26 Jun 2020 08:14:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:14:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:14:44: #1 tags after filtering in treatment: 24034458 INFO @ Fri, 26 Jun 2020 08:14:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:14:44: #1 finished! INFO @ Fri, 26 Jun 2020 08:14:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:14:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:14:45: #2 number of paired peaks: 154 WARNING @ Fri, 26 Jun 2020 08:14:45: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 26 Jun 2020 08:14:45: start model_add_line... INFO @ Fri, 26 Jun 2020 08:14:45: start X-correlation... INFO @ Fri, 26 Jun 2020 08:14:45: end of X-cor INFO @ Fri, 26 Jun 2020 08:14:45: #2 finished! INFO @ Fri, 26 Jun 2020 08:14:45: #2 predicted fragment length is 145 bps INFO @ Fri, 26 Jun 2020 08:14:45: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 26 Jun 2020 08:14:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.10_model.r INFO @ Fri, 26 Jun 2020 08:14:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:14:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:14:46: 20000000 INFO @ Fri, 26 Jun 2020 08:14:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:14:51: 21000000 INFO @ Fri, 26 Jun 2020 08:14:56: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:15:02: 23000000 INFO @ Fri, 26 Jun 2020 08:15:07: 24000000 INFO @ Fri, 26 Jun 2020 08:15:07: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:15:07: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:15:07: #1 total tags in treatment: 24034458 INFO @ Fri, 26 Jun 2020 08:15:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:15:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:15:08: #1 tags after filtering in treatment: 24034458 INFO @ Fri, 26 Jun 2020 08:15:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:15:08: #1 finished! INFO @ Fri, 26 Jun 2020 08:15:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:15:09: #2 number of paired peaks: 154 WARNING @ Fri, 26 Jun 2020 08:15:09: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 26 Jun 2020 08:15:09: start model_add_line... INFO @ Fri, 26 Jun 2020 08:15:10: start X-correlation... INFO @ Fri, 26 Jun 2020 08:15:10: end of X-cor INFO @ Fri, 26 Jun 2020 08:15:10: #2 finished! INFO @ Fri, 26 Jun 2020 08:15:10: #2 predicted fragment length is 145 bps INFO @ Fri, 26 Jun 2020 08:15:10: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 26 Jun 2020 08:15:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.20_model.r INFO @ Fri, 26 Jun 2020 08:15:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:15:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:15:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:15:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:15:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.05_summits.bed INFO @ Fri, 26 Jun 2020 08:15:11: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2991 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:15:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:15:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:15:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:15:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.10_summits.bed INFO @ Fri, 26 Jun 2020 08:15:45: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1918 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:15:50: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:16:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:16:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:16:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2068662/SRX2068662.20_summits.bed INFO @ Fri, 26 Jun 2020 08:16:16: Done! BigWig に変換しました。 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1176 records, 4 fields): 3 millis CompletedMACS2peakCalling