Job ID = 6527575 SRX = SRX1144604 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:06:36 prefetch.2.10.7: 1) Downloading 'SRR2157966'... 2020-06-29T13:06:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:11:53 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:11:53 prefetch.2.10.7: 1) 'SRR2157966' was downloaded successfully 2020-06-29T13:12:44 prefetch.2.10.7: 'SRR2157966' has 10 unresolved dependencies 2020-06-29T13:12:44 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-29T13:12:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:12:54 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:12:54 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:12:54 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-29T13:12:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:13:11 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:13:11 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:13:11 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-29T13:13:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:13:26 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:13:26 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:13:26 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-29T13:13:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:13:42 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:13:42 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:13:42 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-29T13:13:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:13:55 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:13:55 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:13:55 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-29T13:13:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:14:12 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:14:12 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:14:12 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-29T13:14:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:14:27 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:14:27 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:14:27 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-29T13:14:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:14:37 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:14:37 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:14:37 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-29T13:14:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:14:47 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:14:47 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-29T13:14:47 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-29T13:14:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:14:56 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:14:56 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 52299212 spots for SRR2157966/SRR2157966.sra Written 52299212 spots for SRR2157966/SRR2157966.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: 00:08:35 52299212 reads; of these: 52299212 (100.00%) were unpaired; of these: 26423991 (50.52%) aligned 0 times 20509400 (39.22%) aligned exactly 1 time 5365821 (10.26%) aligned >1 times 49.48% overall alignment rate Time searching: 00:08:35 Overall time: 00:08:35 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] 5554720 / 25875221 = 0.2147 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 22:41:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.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 22:41:34: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:41:34: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:41:40: 1000000 INFO @ Mon, 29 Jun 2020 22:41:47: 2000000 INFO @ Mon, 29 Jun 2020 22:41:53: 3000000 INFO @ Mon, 29 Jun 2020 22:42:00: 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 22:42:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.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 22:42:04: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:42:04: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:42:07: 5000000 INFO @ Mon, 29 Jun 2020 22:42:10: 1000000 INFO @ Mon, 29 Jun 2020 22:42:14: 6000000 INFO @ Mon, 29 Jun 2020 22:42:16: 2000000 INFO @ Mon, 29 Jun 2020 22:42:21: 7000000 INFO @ Mon, 29 Jun 2020 22:42:23: 3000000 INFO @ Mon, 29 Jun 2020 22:42:28: 8000000 INFO @ Mon, 29 Jun 2020 22:42:29: 4000000 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 22:42:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.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 22:42:34: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:42:34: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:42:35: 9000000 INFO @ Mon, 29 Jun 2020 22:42:36: 5000000 INFO @ Mon, 29 Jun 2020 22:42:40: 1000000 INFO @ Mon, 29 Jun 2020 22:42:42: 10000000 INFO @ Mon, 29 Jun 2020 22:42:42: 6000000 INFO @ Mon, 29 Jun 2020 22:42:47: 2000000 INFO @ Mon, 29 Jun 2020 22:42:49: 11000000 INFO @ Mon, 29 Jun 2020 22:42:49: 7000000 INFO @ Mon, 29 Jun 2020 22:42:54: 3000000 INFO @ Mon, 29 Jun 2020 22:42:56: 8000000 INFO @ Mon, 29 Jun 2020 22:42:56: 12000000 INFO @ Mon, 29 Jun 2020 22:43:00: 4000000 INFO @ Mon, 29 Jun 2020 22:43:02: 9000000 INFO @ Mon, 29 Jun 2020 22:43:03: 13000000 INFO @ Mon, 29 Jun 2020 22:43:07: 5000000 INFO @ Mon, 29 Jun 2020 22:43:09: 10000000 INFO @ Mon, 29 Jun 2020 22:43:10: 14000000 INFO @ Mon, 29 Jun 2020 22:43:13: 6000000 INFO @ Mon, 29 Jun 2020 22:43:15: 11000000 INFO @ Mon, 29 Jun 2020 22:43:17: 15000000 INFO @ Mon, 29 Jun 2020 22:43:20: 7000000 INFO @ Mon, 29 Jun 2020 22:43:22: 12000000 INFO @ Mon, 29 Jun 2020 22:43:25: 16000000 INFO @ Mon, 29 Jun 2020 22:43:27: 8000000 INFO @ Mon, 29 Jun 2020 22:43:29: 13000000 INFO @ Mon, 29 Jun 2020 22:43:32: 17000000 INFO @ Mon, 29 Jun 2020 22:43:33: 9000000 INFO @ Mon, 29 Jun 2020 22:43:36: 14000000 INFO @ Mon, 29 Jun 2020 22:43:39: 18000000 INFO @ Mon, 29 Jun 2020 22:43:40: 10000000 INFO @ Mon, 29 Jun 2020 22:43:42: 15000000 INFO @ Mon, 29 Jun 2020 22:43:46: 19000000 INFO @ Mon, 29 Jun 2020 22:43:46: 11000000 INFO @ Mon, 29 Jun 2020 22:43:49: 16000000 INFO @ Mon, 29 Jun 2020 22:43:53: 12000000 INFO @ Mon, 29 Jun 2020 22:43:54: 20000000 INFO @ Mon, 29 Jun 2020 22:43:56: 17000000 INFO @ Mon, 29 Jun 2020 22:43:56: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:43:56: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:43:56: #1 total tags in treatment: 20320501 INFO @ Mon, 29 Jun 2020 22:43:56: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:43:56: #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 22:43:56: #1 tags after filtering in treatment: 20320501 INFO @ Mon, 29 Jun 2020 22:43:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:43:56: #1 finished! INFO @ Mon, 29 Jun 2020 22:43:56: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:43:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:43:58: #2 number of paired peaks: 55 WARNING @ Mon, 29 Jun 2020 22:43:58: Too few paired peaks (55) 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 22:43:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.05_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/SRX1144604/SRX1144604.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:44:00: 13000000 INFO @ Mon, 29 Jun 2020 22:44:02: 18000000 INFO @ Mon, 29 Jun 2020 22:44:06: 14000000 INFO @ Mon, 29 Jun 2020 22:44:09: 19000000 INFO @ Mon, 29 Jun 2020 22:44:12: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:44:15: 20000000 INFO @ Mon, 29 Jun 2020 22:44:18: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:44:18: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:44:18: #1 total tags in treatment: 20320501 INFO @ Mon, 29 Jun 2020 22:44:18: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:44:18: #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 22:44:18: #1 tags after filtering in treatment: 20320501 INFO @ Mon, 29 Jun 2020 22:44:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:44:18: #1 finished! INFO @ Mon, 29 Jun 2020 22:44:18: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:44:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:44:19: 16000000 INFO @ Mon, 29 Jun 2020 22:44:19: #2 number of paired peaks: 55 WARNING @ Mon, 29 Jun 2020 22:44:19: Too few paired peaks (55) 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 22:44:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.10_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/SRX1144604/SRX1144604.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:44:24: 17000000 INFO @ Mon, 29 Jun 2020 22:44:30: 18000000 INFO @ Mon, 29 Jun 2020 22:44:36: 19000000 INFO @ Mon, 29 Jun 2020 22:44:42: 20000000 INFO @ Mon, 29 Jun 2020 22:44:44: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:44:44: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:44:44: #1 total tags in treatment: 20320501 INFO @ Mon, 29 Jun 2020 22:44:44: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:44:44: #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 22:44:44: #1 tags after filtering in treatment: 20320501 INFO @ Mon, 29 Jun 2020 22:44:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:44:44: #1 finished! INFO @ Mon, 29 Jun 2020 22:44:44: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:44:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:44:45: #2 number of paired peaks: 55 WARNING @ Mon, 29 Jun 2020 22:44:45: Too few paired peaks (55) 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 22:44:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.20_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/SRX1144604/SRX1144604.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX1144604/SRX1144604.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。