Job ID = 6527564 SRX = SRX1115698 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:31:56 prefetch.2.10.7: 1) Downloading 'SRR2124127'... 2020-06-29T12:31:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:35:15 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:35:15 prefetch.2.10.7: 1) 'SRR2124127' was downloaded successfully 2020-06-29T12:36:06 prefetch.2.10.7: 'SRR2124127' has 10 unresolved dependencies 2020-06-29T12:36:06 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-29T12:36:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:36:22 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:36:22 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:36:22 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-29T12:36:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:36:38 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:36:38 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:36:38 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-29T12:36:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:36:46 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:36:46 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:36:46 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-29T12:36:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:37:04 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:37:04 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:37:04 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-29T12:37:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:37:22 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:37:22 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:37:22 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-29T12:37:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:37:38 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:37:38 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:37:38 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-29T12:37:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:37:52 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:37:52 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:37:52 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-29T12:37:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:38:05 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:38:05 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:38:05 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-29T12:38:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:38:14 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:38:14 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T12:38:14 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-29T12:38:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:38:25 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:38:25 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 27426213 spots for SRR2124127/SRR2124127.sra Written 27426213 spots for SRR2124127/SRR2124127.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: 00:08:19 27426213 reads; of these: 27426213 (100.00%) were unpaired; of these: 865626 (3.16%) aligned 0 times 20164287 (73.52%) aligned exactly 1 time 6396300 (23.32%) aligned >1 times 96.84% overall alignment rate Time searching: 00:08:19 Overall time: 00:08:19 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 12 files... [bam_rmdupse_core] 2713653 / 26560587 = 0.1022 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 22:02:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.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 22:02:57: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:02:57: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:03:03: 1000000 INFO @ Mon, 29 Jun 2020 22:03:10: 2000000 INFO @ Mon, 29 Jun 2020 22:03:16: 3000000 INFO @ Mon, 29 Jun 2020 22:03:22: 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 @ Mon, 29 Jun 2020 22:03:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.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 22:03:27: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:03:27: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:03:28: 5000000 INFO @ Mon, 29 Jun 2020 22:03:34: 1000000 INFO @ Mon, 29 Jun 2020 22:03:35: 6000000 INFO @ Mon, 29 Jun 2020 22:03:40: 2000000 INFO @ Mon, 29 Jun 2020 22:03:41: 7000000 INFO @ Mon, 29 Jun 2020 22:03:47: 3000000 INFO @ Mon, 29 Jun 2020 22:03:48: 8000000 INFO @ Mon, 29 Jun 2020 22:03:53: 4000000 INFO @ Mon, 29 Jun 2020 22:03:54: 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 @ Mon, 29 Jun 2020 22:03:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.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 22:03:57: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:03:57: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:04:00: 5000000 INFO @ Mon, 29 Jun 2020 22:04:01: 10000000 INFO @ Mon, 29 Jun 2020 22:04:05: 1000000 INFO @ Mon, 29 Jun 2020 22:04:07: 6000000 INFO @ Mon, 29 Jun 2020 22:04:07: 11000000 INFO @ Mon, 29 Jun 2020 22:04:12: 2000000 INFO @ Mon, 29 Jun 2020 22:04:14: 12000000 INFO @ Mon, 29 Jun 2020 22:04:15: 7000000 INFO @ Mon, 29 Jun 2020 22:04:20: 3000000 INFO @ Mon, 29 Jun 2020 22:04:20: 13000000 INFO @ Mon, 29 Jun 2020 22:04:22: 8000000 INFO @ Mon, 29 Jun 2020 22:04:27: 14000000 INFO @ Mon, 29 Jun 2020 22:04:27: 4000000 INFO @ Mon, 29 Jun 2020 22:04:30: 9000000 INFO @ Mon, 29 Jun 2020 22:04:33: 15000000 INFO @ Mon, 29 Jun 2020 22:04:34: 5000000 INFO @ Mon, 29 Jun 2020 22:04:37: 10000000 INFO @ Mon, 29 Jun 2020 22:04:40: 16000000 INFO @ Mon, 29 Jun 2020 22:04:42: 6000000 INFO @ Mon, 29 Jun 2020 22:04:45: 11000000 INFO @ Mon, 29 Jun 2020 22:04:46: 17000000 INFO @ Mon, 29 Jun 2020 22:04:50: 7000000 INFO @ Mon, 29 Jun 2020 22:04:52: 12000000 INFO @ Mon, 29 Jun 2020 22:04:53: 18000000 INFO @ Mon, 29 Jun 2020 22:04:57: 8000000 INFO @ Mon, 29 Jun 2020 22:04:59: 19000000 INFO @ Mon, 29 Jun 2020 22:05:00: 13000000 INFO @ Mon, 29 Jun 2020 22:05:05: 9000000 INFO @ Mon, 29 Jun 2020 22:05:06: 20000000 INFO @ Mon, 29 Jun 2020 22:05:07: 14000000 INFO @ Mon, 29 Jun 2020 22:05:13: 10000000 INFO @ Mon, 29 Jun 2020 22:05:14: 21000000 INFO @ Mon, 29 Jun 2020 22:05:15: 15000000 INFO @ Mon, 29 Jun 2020 22:05:20: 11000000 INFO @ Mon, 29 Jun 2020 22:05:21: 22000000 INFO @ Mon, 29 Jun 2020 22:05:23: 16000000 INFO @ Mon, 29 Jun 2020 22:05:28: 12000000 INFO @ Mon, 29 Jun 2020 22:05:28: 23000000 INFO @ Mon, 29 Jun 2020 22:05:30: 17000000 INFO @ Mon, 29 Jun 2020 22:05:33: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 22:05:33: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 22:05:33: #1 total tags in treatment: 23846934 INFO @ Mon, 29 Jun 2020 22:05:33: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:05:33: #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 22:05:34: #1 tags after filtering in treatment: 23846934 INFO @ Mon, 29 Jun 2020 22:05:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:05:34: #1 finished! INFO @ Mon, 29 Jun 2020 22:05:34: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:05:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:05:35: 13000000 INFO @ Mon, 29 Jun 2020 22:05:35: #2 number of paired peaks: 9 WARNING @ Mon, 29 Jun 2020 22:05:35: Too few paired peaks (9) 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 22:05:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.05_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/SRX1115698/SRX1115698.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:05:38: 18000000 INFO @ Mon, 29 Jun 2020 22:05:43: 14000000 INFO @ Mon, 29 Jun 2020 22:05:45: 19000000 INFO @ Mon, 29 Jun 2020 22:05:50: 15000000 INFO @ Mon, 29 Jun 2020 22:05:53: 20000000 INFO @ Mon, 29 Jun 2020 22:05:57: 16000000 INFO @ Mon, 29 Jun 2020 22:06:00: 21000000 INFO @ Mon, 29 Jun 2020 22:06:05: 17000000 INFO @ Mon, 29 Jun 2020 22:06:07: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:06:12: 18000000 INFO @ Mon, 29 Jun 2020 22:06:15: 23000000 INFO @ Mon, 29 Jun 2020 22:06:20: 19000000 INFO @ Mon, 29 Jun 2020 22:06:21: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 22:06:21: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 22:06:21: #1 total tags in treatment: 23846934 INFO @ Mon, 29 Jun 2020 22:06:21: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:06:21: #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 22:06:21: #1 tags after filtering in treatment: 23846934 INFO @ Mon, 29 Jun 2020 22:06:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:06:21: #1 finished! INFO @ Mon, 29 Jun 2020 22:06:21: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:06:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:06:23: #2 number of paired peaks: 9 WARNING @ Mon, 29 Jun 2020 22:06:23: Too few paired peaks (9) 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 22:06:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.10_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/SRX1115698/SRX1115698.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:06:27: 20000000 INFO @ Mon, 29 Jun 2020 22:06:33: 21000000 INFO @ Mon, 29 Jun 2020 22:06:40: 22000000 INFO @ Mon, 29 Jun 2020 22:06:46: 23000000 INFO @ Mon, 29 Jun 2020 22:06:52: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 22:06:52: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 22:06:52: #1 total tags in treatment: 23846934 INFO @ Mon, 29 Jun 2020 22:06:52: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:06:52: #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 22:06:53: #1 tags after filtering in treatment: 23846934 INFO @ Mon, 29 Jun 2020 22:06:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:06:53: #1 finished! INFO @ Mon, 29 Jun 2020 22:06:53: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:06:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:06:54: #2 number of paired peaks: 9 WARNING @ Mon, 29 Jun 2020 22:06:54: Too few paired peaks (9) 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 22:06:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.20_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/SRX1115698/SRX1115698.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1115698/SRX1115698.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。