Job ID = 6451811 SRX = ERX011424 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:13:32 prefetch.2.10.7: 1) Downloading 'ERR031145'... 2020-06-21T07:13:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:15:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:15:32 prefetch.2.10.7: 'ERR031145' is valid 2020-06-21T07:15:32 prefetch.2.10.7: 1) 'ERR031145' was downloaded successfully 2020-06-21T07:16:24 prefetch.2.10.7: 'ERR031145' has 10 unresolved dependencies 2020-06-21T07:16:24 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T07:16:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:16:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:16:40 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:16:40 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T07:16:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:16:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:16:56 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:16:56 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T07:16:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:17:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:17:09 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:17:09 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T07:17:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:17:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:17:25 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:17:25 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T07:17:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:17:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:17:43 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:17:43 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T07:17:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:17:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:17:59 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:17:59 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T07:17:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:18:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:18:12 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:18:12 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T07:18:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:18:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:18:25 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:18:25 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T07:18:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:18:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:18:39 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:18:39 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T07:18:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:18:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:18:55 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 25592798 spots for ERR031145/ERR031145.sra Written 25592798 spots for ERR031145/ERR031145.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: 00:05:21 25592798 reads; of these: 25592798 (100.00%) were unpaired; of these: 977154 (3.82%) aligned 0 times 17765551 (69.42%) aligned exactly 1 time 6850093 (26.77%) aligned >1 times 96.18% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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] 8089857 / 24615644 = 0.3286 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 16:29:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.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 16:29:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:29:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:30:03: 1000000 INFO @ Sun, 21 Jun 2020 16:30:08: 2000000 INFO @ Sun, 21 Jun 2020 16:30:14: 3000000 INFO @ Sun, 21 Jun 2020 16:30:19: 4000000 INFO @ Sun, 21 Jun 2020 16:30:24: 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 16:30:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.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 16:30:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:30:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:30:29: 6000000 INFO @ Sun, 21 Jun 2020 16:30:34: 1000000 INFO @ Sun, 21 Jun 2020 16:30:35: 7000000 INFO @ Sun, 21 Jun 2020 16:30:40: 2000000 INFO @ Sun, 21 Jun 2020 16:30:41: 8000000 INFO @ Sun, 21 Jun 2020 16:30:46: 3000000 INFO @ Sun, 21 Jun 2020 16:30:47: 9000000 INFO @ Sun, 21 Jun 2020 16:30:52: 4000000 INFO @ Sun, 21 Jun 2020 16:30:53: 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 16:30:58: 5000000 INFO @ Sun, 21 Jun 2020 16:30:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.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 16:30:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:30:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:30:59: 11000000 INFO @ Sun, 21 Jun 2020 16:31:04: 6000000 INFO @ Sun, 21 Jun 2020 16:31:04: 1000000 INFO @ Sun, 21 Jun 2020 16:31:05: 12000000 INFO @ Sun, 21 Jun 2020 16:31:10: 7000000 INFO @ Sun, 21 Jun 2020 16:31:10: 2000000 INFO @ Sun, 21 Jun 2020 16:31:12: 13000000 INFO @ Sun, 21 Jun 2020 16:31:16: 8000000 INFO @ Sun, 21 Jun 2020 16:31:16: 3000000 INFO @ Sun, 21 Jun 2020 16:31:18: 14000000 INFO @ Sun, 21 Jun 2020 16:31:22: 9000000 INFO @ Sun, 21 Jun 2020 16:31:22: 4000000 INFO @ Sun, 21 Jun 2020 16:31:24: 15000000 INFO @ Sun, 21 Jun 2020 16:31:28: 10000000 INFO @ Sun, 21 Jun 2020 16:31:28: 5000000 INFO @ Sun, 21 Jun 2020 16:31:30: 16000000 INFO @ Sun, 21 Jun 2020 16:31:34: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:31:34: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:31:34: #1 total tags in treatment: 16525787 INFO @ Sun, 21 Jun 2020 16:31:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:31:34: #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 16:31:34: 11000000 INFO @ Sun, 21 Jun 2020 16:31:34: 6000000 INFO @ Sun, 21 Jun 2020 16:31:34: #1 tags after filtering in treatment: 16525787 INFO @ Sun, 21 Jun 2020 16:31:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:31:34: #1 finished! INFO @ Sun, 21 Jun 2020 16:31:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:31:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:31:35: #2 number of paired peaks: 824 WARNING @ Sun, 21 Jun 2020 16:31:35: Fewer paired peaks (824) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 824 pairs to build model! INFO @ Sun, 21 Jun 2020 16:31:35: start model_add_line... INFO @ Sun, 21 Jun 2020 16:31:35: start X-correlation... INFO @ Sun, 21 Jun 2020 16:31:35: end of X-cor INFO @ Sun, 21 Jun 2020 16:31:35: #2 finished! INFO @ Sun, 21 Jun 2020 16:31:35: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 16:31:35: #2 alternative fragment length(s) may be 4,49,65,90 bps INFO @ Sun, 21 Jun 2020 16:31:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.05_model.r WARNING @ Sun, 21 Jun 2020 16:31:35: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:31:35: #2 You may need to consider one of the other alternative d(s): 4,49,65,90 WARNING @ Sun, 21 Jun 2020 16:31:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 16:31:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:31:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:31:40: 7000000 INFO @ Sun, 21 Jun 2020 16:31:40: 12000000 INFO @ Sun, 21 Jun 2020 16:31:46: 8000000 INFO @ Sun, 21 Jun 2020 16:31:46: 13000000 INFO @ Sun, 21 Jun 2020 16:31:52: 9000000 INFO @ Sun, 21 Jun 2020 16:31:53: 14000000 INFO @ Sun, 21 Jun 2020 16:31:58: 10000000 INFO @ Sun, 21 Jun 2020 16:31:59: 15000000 INFO @ Sun, 21 Jun 2020 16:32:04: 11000000 INFO @ Sun, 21 Jun 2020 16:32:05: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:32:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:32:08: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:32:08: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:32:08: #1 total tags in treatment: 16525787 INFO @ Sun, 21 Jun 2020 16:32:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:32:08: #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 16:32:09: #1 tags after filtering in treatment: 16525787 INFO @ Sun, 21 Jun 2020 16:32:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:32:09: #1 finished! INFO @ Sun, 21 Jun 2020 16:32:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:32:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:32:10: #2 number of paired peaks: 824 WARNING @ Sun, 21 Jun 2020 16:32:10: Fewer paired peaks (824) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 824 pairs to build model! INFO @ Sun, 21 Jun 2020 16:32:10: start model_add_line... INFO @ Sun, 21 Jun 2020 16:32:10: start X-correlation... INFO @ Sun, 21 Jun 2020 16:32:10: end of X-cor INFO @ Sun, 21 Jun 2020 16:32:10: #2 finished! INFO @ Sun, 21 Jun 2020 16:32:10: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 16:32:10: #2 alternative fragment length(s) may be 4,49,65,90 bps INFO @ Sun, 21 Jun 2020 16:32:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.10_model.r WARNING @ Sun, 21 Jun 2020 16:32:10: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:32:10: #2 You may need to consider one of the other alternative d(s): 4,49,65,90 WARNING @ Sun, 21 Jun 2020 16:32:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 16:32:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:32:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:32:10: 12000000 INFO @ Sun, 21 Jun 2020 16:32:16: 13000000 INFO @ Sun, 21 Jun 2020 16:32:21: 14000000 INFO @ Sun, 21 Jun 2020 16:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.05_summits.bed INFO @ Sun, 21 Jun 2020 16:32:22: Done! pass1 - making usageList (692 chroms): 2 millis pass2 - checking and writing primary data (4438 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:32:27: 15000000 INFO @ Sun, 21 Jun 2020 16:32:32: 16000000 INFO @ Sun, 21 Jun 2020 16:32:35: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:32:35: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:32:35: #1 total tags in treatment: 16525787 INFO @ Sun, 21 Jun 2020 16:32:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:32:35: #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 16:32:36: #1 tags after filtering in treatment: 16525787 INFO @ Sun, 21 Jun 2020 16:32:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:32:36: #1 finished! INFO @ Sun, 21 Jun 2020 16:32:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:32:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:32:37: #2 number of paired peaks: 824 WARNING @ Sun, 21 Jun 2020 16:32:37: Fewer paired peaks (824) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 824 pairs to build model! INFO @ Sun, 21 Jun 2020 16:32:37: start model_add_line... INFO @ Sun, 21 Jun 2020 16:32:37: start X-correlation... INFO @ Sun, 21 Jun 2020 16:32:37: end of X-cor INFO @ Sun, 21 Jun 2020 16:32:37: #2 finished! INFO @ Sun, 21 Jun 2020 16:32:37: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 16:32:37: #2 alternative fragment length(s) may be 4,49,65,90 bps INFO @ Sun, 21 Jun 2020 16:32:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.20_model.r WARNING @ Sun, 21 Jun 2020 16:32:37: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:32:37: #2 You may need to consider one of the other alternative d(s): 4,49,65,90 WARNING @ Sun, 21 Jun 2020 16:32:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 16:32:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:32:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:32:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:32:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:32:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:32:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.10_summits.bed INFO @ Sun, 21 Jun 2020 16:32:56: Done! pass1 - making usageList (572 chroms): 2 millis pass2 - checking and writing primary data (2962 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:33:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:33:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:33:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:33:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011424/ERX011424.20_summits.bed INFO @ Sun, 21 Jun 2020 16:33:22: Done! pass1 - making usageList (449 chroms): 1 millis pass2 - checking and writing primary data (1819 records, 4 fields): 13 millis CompletedMACS2peakCalling