Job ID = 6527571 SRX = SRX113306 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:03:35 prefetch.2.10.7: 1) Downloading 'SRR392912'... 2020-06-29T13:03:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:05:03 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:05:04 prefetch.2.10.7: 'SRR392912' is valid 2020-06-29T13:05:04 prefetch.2.10.7: 1) 'SRR392912' was downloaded successfully Read 9364299 spots for SRR392912/SRR392912.sra Written 9364299 spots for SRR392912/SRR392912.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: 00:02:17 9364299 reads; of these: 9364299 (100.00%) were unpaired; of these: 148743 (1.59%) aligned 0 times 7102723 (75.85%) aligned exactly 1 time 2112833 (22.56%) aligned >1 times 98.41% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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] 1175138 / 9215556 = 0.1275 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 22:12:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.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 22:12:06: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:12:06: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:12:12: 1000000 INFO @ Mon, 29 Jun 2020 22:12:17: 2000000 INFO @ Mon, 29 Jun 2020 22:12:22: 3000000 INFO @ Mon, 29 Jun 2020 22:12:28: 4000000 INFO @ Mon, 29 Jun 2020 22:12:33: 5000000 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 22:12:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.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 22:12:36: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:12:36: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:12:39: 6000000 INFO @ Mon, 29 Jun 2020 22:12:43: 1000000 INFO @ Mon, 29 Jun 2020 22:12:46: 7000000 INFO @ Mon, 29 Jun 2020 22:12:50: 2000000 INFO @ Mon, 29 Jun 2020 22:12:52: 8000000 INFO @ Mon, 29 Jun 2020 22:12:52: #1 tag size is determined as 44 bps INFO @ Mon, 29 Jun 2020 22:12:52: #1 tag size = 44 INFO @ Mon, 29 Jun 2020 22:12:52: #1 total tags in treatment: 8040418 INFO @ Mon, 29 Jun 2020 22:12:52: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:12:52: #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 22:12:52: #1 tags after filtering in treatment: 8040418 INFO @ Mon, 29 Jun 2020 22:12:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:12:52: #1 finished! INFO @ Mon, 29 Jun 2020 22:12:52: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:12:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:12:53: #2 number of paired peaks: 54 WARNING @ Mon, 29 Jun 2020 22:12:53: Too few paired peaks (54) 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 22:12:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.05_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/SRX113306/SRX113306.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:12:57: 3000000 INFO @ Mon, 29 Jun 2020 22:13:04: 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 22:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.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 22:13:06: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:13:06: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:13:10: 5000000 INFO @ Mon, 29 Jun 2020 22:13:13: 1000000 INFO @ Mon, 29 Jun 2020 22:13:18: 6000000 INFO @ Mon, 29 Jun 2020 22:13:20: 2000000 INFO @ Mon, 29 Jun 2020 22:13:25: 7000000 INFO @ Mon, 29 Jun 2020 22:13:27: 3000000 INFO @ Mon, 29 Jun 2020 22:13:32: 8000000 INFO @ Mon, 29 Jun 2020 22:13:32: #1 tag size is determined as 44 bps INFO @ Mon, 29 Jun 2020 22:13:32: #1 tag size = 44 INFO @ Mon, 29 Jun 2020 22:13:32: #1 total tags in treatment: 8040418 INFO @ Mon, 29 Jun 2020 22:13:32: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:13:32: #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 22:13:32: #1 tags after filtering in treatment: 8040418 INFO @ Mon, 29 Jun 2020 22:13:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:13:32: #1 finished! INFO @ Mon, 29 Jun 2020 22:13:32: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:13:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:13:32: #2 number of paired peaks: 54 WARNING @ Mon, 29 Jun 2020 22:13:32: Too few paired peaks (54) 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 22:13:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.10_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/SRX113306/SRX113306.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:13:34: 4000000 INFO @ Mon, 29 Jun 2020 22:13:40: 5000000 INFO @ Mon, 29 Jun 2020 22:13:47: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:13:53: 7000000 INFO @ Mon, 29 Jun 2020 22:14:00: 8000000 INFO @ Mon, 29 Jun 2020 22:14:00: #1 tag size is determined as 44 bps INFO @ Mon, 29 Jun 2020 22:14:00: #1 tag size = 44 INFO @ Mon, 29 Jun 2020 22:14:00: #1 total tags in treatment: 8040418 INFO @ Mon, 29 Jun 2020 22:14:00: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:14:00: #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 22:14:00: #1 tags after filtering in treatment: 8040418 INFO @ Mon, 29 Jun 2020 22:14:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:14:00: #1 finished! INFO @ Mon, 29 Jun 2020 22:14:00: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:14:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:14:01: #2 number of paired peaks: 54 WARNING @ Mon, 29 Jun 2020 22:14:01: Too few paired peaks (54) 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 22:14:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.20_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/SRX113306/SRX113306.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX113306/SRX113306.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。