Job ID = 6451814 SRX = ERX011425 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:07:33 prefetch.2.10.7: 1) Downloading 'ERR031146'... 2020-06-21T07:07:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:09:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:09:48 prefetch.2.10.7: 'ERR031146' is valid 2020-06-21T07:09:48 prefetch.2.10.7: 1) 'ERR031146' was downloaded successfully 2020-06-21T07:10:39 prefetch.2.10.7: 'ERR031146' has 10 unresolved dependencies 2020-06-21T07:10:39 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T07:10:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:10:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:10:59 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:10:59 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T07:10:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:11:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:11:16 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:11:16 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T07:11:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:11:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:11:29 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:11:29 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T07:11:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:11:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:11:46 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:11:46 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T07:11:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:12:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:12:13 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:12:13 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T07:12:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:12:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:12:31 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:12:31 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T07:12:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:12:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:12:45 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:12:45 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T07:12:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:12:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:12:58 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:12:58 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T07:12:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:13:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:13:11 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:13:11 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T07:13:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:13:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:13:35 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 30754969 spots for ERR031146/ERR031146.sra Written 30754969 spots for ERR031146/ERR031146.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: 00:00:01 Multiseed full-index search: 00:06:42 30754969 reads; of these: 30754969 (100.00%) were unpaired; of these: 1076379 (3.50%) aligned 0 times 20405395 (66.35%) aligned exactly 1 time 9273195 (30.15%) aligned >1 times 96.50% overall alignment rate Time searching: 00:06:44 Overall time: 00:06:44 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] 13323987 / 29678590 = 0.4489 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 16:27:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.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 16:27:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:27:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:27:18: 1000000 INFO @ Sun, 21 Jun 2020 16:27:25: 2000000 INFO @ Sun, 21 Jun 2020 16:27:31: 3000000 INFO @ Sun, 21 Jun 2020 16:27:37: 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 16:27:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.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 16:27:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:27:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:27:43: 5000000 INFO @ Sun, 21 Jun 2020 16:27:49: 1000000 INFO @ Sun, 21 Jun 2020 16:27:50: 6000000 INFO @ Sun, 21 Jun 2020 16:27:56: 2000000 INFO @ Sun, 21 Jun 2020 16:27:56: 7000000 INFO @ Sun, 21 Jun 2020 16:28:02: 3000000 INFO @ Sun, 21 Jun 2020 16:28:03: 8000000 INFO @ Sun, 21 Jun 2020 16:28:09: 4000000 INFO @ Sun, 21 Jun 2020 16:28:09: 9000000 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 16:28:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.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 16:28:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:28:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:28:16: 10000000 INFO @ Sun, 21 Jun 2020 16:28:16: 5000000 INFO @ Sun, 21 Jun 2020 16:28:20: 1000000 INFO @ Sun, 21 Jun 2020 16:28:22: 11000000 INFO @ Sun, 21 Jun 2020 16:28:22: 6000000 INFO @ Sun, 21 Jun 2020 16:28:26: 2000000 INFO @ Sun, 21 Jun 2020 16:28:29: 7000000 INFO @ Sun, 21 Jun 2020 16:28:29: 12000000 INFO @ Sun, 21 Jun 2020 16:28:33: 3000000 INFO @ Sun, 21 Jun 2020 16:28:35: 8000000 INFO @ Sun, 21 Jun 2020 16:28:36: 13000000 INFO @ Sun, 21 Jun 2020 16:28:40: 4000000 INFO @ Sun, 21 Jun 2020 16:28:42: 9000000 INFO @ Sun, 21 Jun 2020 16:28:42: 14000000 INFO @ Sun, 21 Jun 2020 16:28:46: 5000000 INFO @ Sun, 21 Jun 2020 16:28:48: 10000000 INFO @ Sun, 21 Jun 2020 16:28:49: 15000000 INFO @ Sun, 21 Jun 2020 16:28:53: 6000000 INFO @ Sun, 21 Jun 2020 16:28:55: 11000000 INFO @ Sun, 21 Jun 2020 16:28:55: 16000000 INFO @ Sun, 21 Jun 2020 16:28:57: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:28:57: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:28:57: #1 total tags in treatment: 16354603 INFO @ Sun, 21 Jun 2020 16:28:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:28:57: #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 16:28:58: #1 tags after filtering in treatment: 16354602 INFO @ Sun, 21 Jun 2020 16:28:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:28:58: #1 finished! INFO @ Sun, 21 Jun 2020 16:28:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:28:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:28:59: #2 number of paired peaks: 1056 INFO @ Sun, 21 Jun 2020 16:28:59: start model_add_line... INFO @ Sun, 21 Jun 2020 16:28:59: start X-correlation... INFO @ Sun, 21 Jun 2020 16:28:59: end of X-cor INFO @ Sun, 21 Jun 2020 16:28:59: #2 finished! INFO @ Sun, 21 Jun 2020 16:28:59: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 16:28:59: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sun, 21 Jun 2020 16:28:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.05_model.r WARNING @ Sun, 21 Jun 2020 16:28:59: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:28:59: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sun, 21 Jun 2020 16:28:59: #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 16:28:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:28:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:28:59: 7000000 INFO @ Sun, 21 Jun 2020 16:29:01: 12000000 INFO @ Sun, 21 Jun 2020 16:29:06: 8000000 INFO @ Sun, 21 Jun 2020 16:29:08: 13000000 INFO @ Sun, 21 Jun 2020 16:29:12: 9000000 INFO @ Sun, 21 Jun 2020 16:29:15: 14000000 INFO @ Sun, 21 Jun 2020 16:29:19: 10000000 INFO @ Sun, 21 Jun 2020 16:29:21: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:29:25: 11000000 INFO @ Sun, 21 Jun 2020 16:29:27: 16000000 INFO @ Sun, 21 Jun 2020 16:29:29: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:29:29: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:29:29: #1 total tags in treatment: 16354603 INFO @ Sun, 21 Jun 2020 16:29:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:29:29: #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 16:29:30: #1 tags after filtering in treatment: 16354602 INFO @ Sun, 21 Jun 2020 16:29:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:29:30: #1 finished! INFO @ Sun, 21 Jun 2020 16:29:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:29:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:29:31: #2 number of paired peaks: 1056 INFO @ Sun, 21 Jun 2020 16:29:31: start model_add_line... INFO @ Sun, 21 Jun 2020 16:29:31: start X-correlation... INFO @ Sun, 21 Jun 2020 16:29:31: end of X-cor INFO @ Sun, 21 Jun 2020 16:29:31: #2 finished! INFO @ Sun, 21 Jun 2020 16:29:31: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 16:29:31: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sun, 21 Jun 2020 16:29:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.10_model.r WARNING @ Sun, 21 Jun 2020 16:29:31: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:29:31: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sun, 21 Jun 2020 16:29:31: #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 16:29:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:29:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:29:31: 12000000 INFO @ Sun, 21 Jun 2020 16:29:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:29:38: 13000000 INFO @ Sun, 21 Jun 2020 16:29:44: 14000000 INFO @ Sun, 21 Jun 2020 16:29:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:29:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:29:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.05_summits.bed INFO @ Sun, 21 Jun 2020 16:29:49: Done! INFO @ Sun, 21 Jun 2020 16:29:50: 15000000 pass1 - making usageList (721 chroms): 3 millis pass2 - checking and writing primary data (4509 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:29:57: 16000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:29:59: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:29:59: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:29:59: #1 total tags in treatment: 16354603 INFO @ Sun, 21 Jun 2020 16:29:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:29:59: #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 16:30:00: #1 tags after filtering in treatment: 16354602 INFO @ Sun, 21 Jun 2020 16:30:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:30:00: #1 finished! INFO @ Sun, 21 Jun 2020 16:30:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:30:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:30:01: #2 number of paired peaks: 1056 INFO @ Sun, 21 Jun 2020 16:30:01: start model_add_line... INFO @ Sun, 21 Jun 2020 16:30:01: start X-correlation... INFO @ Sun, 21 Jun 2020 16:30:01: end of X-cor INFO @ Sun, 21 Jun 2020 16:30:01: #2 finished! INFO @ Sun, 21 Jun 2020 16:30:01: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 16:30:01: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sun, 21 Jun 2020 16:30:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.20_model.r WARNING @ Sun, 21 Jun 2020 16:30:01: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:30:01: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sun, 21 Jun 2020 16:30:01: #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 16:30:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:30:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:30:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:30:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:30:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:30:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.10_summits.bed INFO @ Sun, 21 Jun 2020 16:30:20: Done! pass1 - making usageList (597 chroms): 1 millis pass2 - checking and writing primary data (3049 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:30:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:30:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:30:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:30:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011425/ERX011425.20_summits.bed INFO @ Sun, 21 Jun 2020 16:30:53: Done! pass1 - making usageList (479 chroms): 1 millis pass2 - checking and writing primary data (2007 records, 4 fields): 16 millis CompletedMACS2peakCalling