Job ID = 6527422 SRX = ERX011407 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:43:20 prefetch.2.10.7: 1) Downloading 'ERR031128'... 2020-06-29T12:43:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:44:22 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:44:22 prefetch.2.10.7: 'ERR031128' is valid 2020-06-29T12:44:22 prefetch.2.10.7: 1) 'ERR031128' was downloaded successfully 2020-06-29T12:45:14 prefetch.2.10.7: 'ERR031128' has 10 unresolved dependencies 2020-06-29T12:45:14 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-29T12:45:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:45:26 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:45:26 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:45:26 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-29T12:45:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:45:40 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:45:40 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:45:40 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-29T12:45:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:45:48 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:45:48 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:45:48 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-29T12:45:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:46:05 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:46:05 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:46:05 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-29T12:46:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:46:23 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:46:23 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:46:23 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-29T12:46:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:46:36 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:46:36 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:46:36 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-29T12:46:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:46:50 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:46:50 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:46:50 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-29T12:46:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:47:03 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:47:04 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:47:04 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-29T12:47:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:47:17 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:47:17 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:47:17 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-29T12:47:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:47:29 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:47:29 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 22619717 spots for ERR031128/ERR031128.sra Written 22619717 spots for ERR031128/ERR031128.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: 00:05:52 22619717 reads; of these: 22619717 (100.00%) were unpaired; of these: 604183 (2.67%) aligned 0 times 16108164 (71.21%) aligned exactly 1 time 5907370 (26.12%) aligned >1 times 97.33% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 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 8 files... [bam_rmdupse_core] 4357846 / 22015534 = 0.1979 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 @ Mon, 29 Jun 2020 22:01:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.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 @ Mon, 29 Jun 2020 22:01:12: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:01:12: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:01:16: 1000000 INFO @ Mon, 29 Jun 2020 22:01:20: 2000000 INFO @ Mon, 29 Jun 2020 22:01:25: 3000000 INFO @ Mon, 29 Jun 2020 22:01:29: 4000000 INFO @ Mon, 29 Jun 2020 22:01:34: 5000000 INFO @ Mon, 29 Jun 2020 22:01:38: 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 @ Mon, 29 Jun 2020 22:01:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.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 @ Mon, 29 Jun 2020 22:01:42: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:01:42: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:01:42: 7000000 INFO @ Mon, 29 Jun 2020 22:01:47: 1000000 INFO @ Mon, 29 Jun 2020 22:01:47: 8000000 INFO @ Mon, 29 Jun 2020 22:01:51: 9000000 INFO @ Mon, 29 Jun 2020 22:01:52: 2000000 INFO @ Mon, 29 Jun 2020 22:01:56: 10000000 INFO @ Mon, 29 Jun 2020 22:01:57: 3000000 INFO @ Mon, 29 Jun 2020 22:02:01: 11000000 INFO @ Mon, 29 Jun 2020 22:02:03: 4000000 INFO @ Mon, 29 Jun 2020 22:02:05: 12000000 INFO @ Mon, 29 Jun 2020 22:02:08: 5000000 INFO @ Mon, 29 Jun 2020 22:02:10: 13000000 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 @ Mon, 29 Jun 2020 22:02:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.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 @ Mon, 29 Jun 2020 22:02:12: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:02:12: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:02:13: 6000000 INFO @ Mon, 29 Jun 2020 22:02:14: 14000000 INFO @ Mon, 29 Jun 2020 22:02:17: 1000000 INFO @ Mon, 29 Jun 2020 22:02:18: 7000000 INFO @ Mon, 29 Jun 2020 22:02:19: 15000000 INFO @ Mon, 29 Jun 2020 22:02:21: 2000000 INFO @ Mon, 29 Jun 2020 22:02:23: 8000000 INFO @ Mon, 29 Jun 2020 22:02:23: 16000000 INFO @ Mon, 29 Jun 2020 22:02:26: 3000000 INFO @ Mon, 29 Jun 2020 22:02:28: 17000000 INFO @ Mon, 29 Jun 2020 22:02:28: 9000000 INFO @ Mon, 29 Jun 2020 22:02:31: 4000000 INFO @ Mon, 29 Jun 2020 22:02:31: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:02:31: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:02:31: #1 total tags in treatment: 17657688 INFO @ Mon, 29 Jun 2020 22:02:31: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:02:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:02:31: #1 tags after filtering in treatment: 17657688 INFO @ Mon, 29 Jun 2020 22:02:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:02:31: #1 finished! INFO @ Mon, 29 Jun 2020 22:02:31: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:02:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:02:32: #2 number of paired peaks: 88 WARNING @ Mon, 29 Jun 2020 22:02:32: Too few paired peaks (88) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Mon, 29 Jun 2020 22:02:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:02:33: 10000000 INFO @ Mon, 29 Jun 2020 22:02:35: 5000000 INFO @ Mon, 29 Jun 2020 22:02:38: 11000000 INFO @ Mon, 29 Jun 2020 22:02:40: 6000000 INFO @ Mon, 29 Jun 2020 22:02:43: 12000000 INFO @ Mon, 29 Jun 2020 22:02:44: 7000000 INFO @ Mon, 29 Jun 2020 22:02:48: 13000000 INFO @ Mon, 29 Jun 2020 22:02:49: 8000000 INFO @ Mon, 29 Jun 2020 22:02:53: 14000000 INFO @ Mon, 29 Jun 2020 22:02:53: 9000000 INFO @ Mon, 29 Jun 2020 22:02:58: 10000000 INFO @ Mon, 29 Jun 2020 22:02:58: 15000000 INFO @ Mon, 29 Jun 2020 22:03:02: 11000000 INFO @ Mon, 29 Jun 2020 22:03:03: 16000000 INFO @ Mon, 29 Jun 2020 22:03:07: 12000000 INFO @ Mon, 29 Jun 2020 22:03:08: 17000000 INFO @ Mon, 29 Jun 2020 22:03:11: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:03:11: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:03:11: #1 total tags in treatment: 17657688 INFO @ Mon, 29 Jun 2020 22:03:11: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:03:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:03:11: 13000000 INFO @ Mon, 29 Jun 2020 22:03:11: #1 tags after filtering in treatment: 17657688 INFO @ Mon, 29 Jun 2020 22:03:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:03:11: #1 finished! INFO @ Mon, 29 Jun 2020 22:03:11: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:03:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:03:12: #2 number of paired peaks: 88 WARNING @ Mon, 29 Jun 2020 22:03:12: Too few paired peaks (88) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Mon, 29 Jun 2020 22:03:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:03:16: 14000000 INFO @ Mon, 29 Jun 2020 22:03:20: 15000000 INFO @ Mon, 29 Jun 2020 22:03:24: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:03:29: 17000000 INFO @ Mon, 29 Jun 2020 22:03:32: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:03:32: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:03:32: #1 total tags in treatment: 17657688 INFO @ Mon, 29 Jun 2020 22:03:32: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:03:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:03:32: #1 tags after filtering in treatment: 17657688 INFO @ Mon, 29 Jun 2020 22:03:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:03:32: #1 finished! INFO @ Mon, 29 Jun 2020 22:03:32: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:03:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:03:33: #2 number of paired peaks: 88 WARNING @ Mon, 29 Jun 2020 22:03:33: Too few paired peaks (88) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Mon, 29 Jun 2020 22:03:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/ERX011407/ERX011407.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。