Job ID = 6527685 SRX = SRX209932 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:13:03 prefetch.2.10.7: 1) Downloading 'SRR631787'... 2020-06-29T13:13:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:14:40 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:14:40 prefetch.2.10.7: 'SRR631787' is valid 2020-06-29T13:14:40 prefetch.2.10.7: 1) 'SRR631787' was downloaded successfully Read 11779768 spots for SRR631787/SRR631787.sra Written 11779768 spots for SRR631787/SRR631787.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: 00:03:09 11779768 reads; of these: 11779768 (100.00%) were unpaired; of these: 959406 (8.14%) aligned 0 times 8581099 (72.85%) aligned exactly 1 time 2239263 (19.01%) aligned >1 times 91.86% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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_rmdupse_core] 1870249 / 10820362 = 0.1728 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 22:23:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.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 22:23:18: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:23:18: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:23:23: 1000000 INFO @ Mon, 29 Jun 2020 22:23:28: 2000000 INFO @ Mon, 29 Jun 2020 22:23:32: 3000000 INFO @ Mon, 29 Jun 2020 22:23:37: 4000000 INFO @ Mon, 29 Jun 2020 22:23:41: 5000000 INFO @ Mon, 29 Jun 2020 22:23:46: 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 22:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.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 22:23:48: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:23:48: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:23:50: 7000000 INFO @ Mon, 29 Jun 2020 22:23:53: 1000000 INFO @ Mon, 29 Jun 2020 22:23:55: 8000000 INFO @ Mon, 29 Jun 2020 22:23:58: 2000000 INFO @ Mon, 29 Jun 2020 22:23:59: #1 tag size is determined as 40 bps INFO @ Mon, 29 Jun 2020 22:23:59: #1 tag size = 40 INFO @ Mon, 29 Jun 2020 22:23:59: #1 total tags in treatment: 8950113 INFO @ Mon, 29 Jun 2020 22:23:59: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:23:59: #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 22:24:00: #1 tags after filtering in treatment: 8950113 INFO @ Mon, 29 Jun 2020 22:24:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:24:00: #1 finished! INFO @ Mon, 29 Jun 2020 22:24:00: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:24:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:24:00: #2 number of paired peaks: 72 WARNING @ Mon, 29 Jun 2020 22:24:00: Too few paired peaks (72) 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 22:24:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:24:02: 3000000 INFO @ Mon, 29 Jun 2020 22:24:07: 4000000 INFO @ Mon, 29 Jun 2020 22:24:11: 5000000 INFO @ Mon, 29 Jun 2020 22:24:16: 6000000 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 22:24:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.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 22:24:18: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:24:18: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:24:20: 7000000 INFO @ Mon, 29 Jun 2020 22:24:23: 1000000 INFO @ Mon, 29 Jun 2020 22:24:25: 8000000 INFO @ Mon, 29 Jun 2020 22:24:28: 2000000 INFO @ Mon, 29 Jun 2020 22:24:30: #1 tag size is determined as 40 bps INFO @ Mon, 29 Jun 2020 22:24:30: #1 tag size = 40 INFO @ Mon, 29 Jun 2020 22:24:30: #1 total tags in treatment: 8950113 INFO @ Mon, 29 Jun 2020 22:24:30: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:24:30: #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 22:24:30: #1 tags after filtering in treatment: 8950113 INFO @ Mon, 29 Jun 2020 22:24:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:24:30: #1 finished! INFO @ Mon, 29 Jun 2020 22:24:30: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:24:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:24:30: #2 number of paired peaks: 72 WARNING @ Mon, 29 Jun 2020 22:24:30: Too few paired peaks (72) 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 22:24:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:24:33: 3000000 INFO @ Mon, 29 Jun 2020 22:24:37: 4000000 INFO @ Mon, 29 Jun 2020 22:24:42: 5000000 INFO @ Mon, 29 Jun 2020 22:24:47: 6000000 INFO @ Mon, 29 Jun 2020 22:24:51: 7000000 INFO @ Mon, 29 Jun 2020 22:24:56: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:25:00: #1 tag size is determined as 40 bps INFO @ Mon, 29 Jun 2020 22:25:00: #1 tag size = 40 INFO @ Mon, 29 Jun 2020 22:25:00: #1 total tags in treatment: 8950113 INFO @ Mon, 29 Jun 2020 22:25:00: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:25:00: #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 22:25:00: #1 tags after filtering in treatment: 8950113 INFO @ Mon, 29 Jun 2020 22:25:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:25:00: #1 finished! INFO @ Mon, 29 Jun 2020 22:25:00: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:25:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:25:01: #2 number of paired peaks: 72 WARNING @ Mon, 29 Jun 2020 22:25:01: Too few paired peaks (72) 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 22:25:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.20_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/SRX209932/SRX209932.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX209932/SRX209932.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。