Job ID = 6527643 SRX = SRX183887 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:54:08 prefetch.2.10.7: 1) Downloading 'SRR557682'... 2020-06-29T12:54:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:55:14 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:55:15 prefetch.2.10.7: 'SRR557682' is valid 2020-06-29T12:55:15 prefetch.2.10.7: 1) 'SRR557682' was downloaded successfully Read 8594417 spots for SRR557682/SRR557682.sra Written 8594417 spots for SRR557682/SRR557682.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: 00:02:21 8594417 reads; of these: 8594417 (100.00%) were unpaired; of these: 172842 (2.01%) aligned 0 times 6515858 (75.82%) aligned exactly 1 time 1905717 (22.17%) aligned >1 times 97.99% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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] 385830 / 8421575 = 0.0458 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 22:01:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.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 22:01:31: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:01:31: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:01:36: 1000000 INFO @ Mon, 29 Jun 2020 22:01:41: 2000000 INFO @ Mon, 29 Jun 2020 22:01:46: 3000000 INFO @ Mon, 29 Jun 2020 22:01:51: 4000000 INFO @ Mon, 29 Jun 2020 22:01:56: 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 22:02:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.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 22:02:00: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:02:00: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:02:01: 6000000 INFO @ Mon, 29 Jun 2020 22:02:06: 1000000 INFO @ Mon, 29 Jun 2020 22:02:07: 7000000 INFO @ Mon, 29 Jun 2020 22:02:12: 2000000 INFO @ Mon, 29 Jun 2020 22:02:12: 8000000 INFO @ Mon, 29 Jun 2020 22:02:13: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:02:13: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:02:13: #1 total tags in treatment: 8035745 INFO @ Mon, 29 Jun 2020 22:02:13: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:02:13: #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 22:02:13: #1 tags after filtering in treatment: 8035745 INFO @ Mon, 29 Jun 2020 22:02:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:02:13: #1 finished! INFO @ Mon, 29 Jun 2020 22:02:13: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:02:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:02:13: #2 number of paired peaks: 29 WARNING @ Mon, 29 Jun 2020 22:02:13: Too few paired peaks (29) 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 22:02:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.05_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/SRX183887/SRX183887.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:02:17: 3000000 INFO @ Mon, 29 Jun 2020 22:02:22: 4000000 INFO @ Mon, 29 Jun 2020 22:02:28: 5000000 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 22:02:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.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 22:02:30: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:02:30: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:02:33: 6000000 INFO @ Mon, 29 Jun 2020 22:02:36: 1000000 INFO @ Mon, 29 Jun 2020 22:02:39: 7000000 INFO @ Mon, 29 Jun 2020 22:02:42: 2000000 INFO @ Mon, 29 Jun 2020 22:02:44: 8000000 INFO @ Mon, 29 Jun 2020 22:02:45: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:02:45: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:02:45: #1 total tags in treatment: 8035745 INFO @ Mon, 29 Jun 2020 22:02:45: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:02:45: #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 22:02:45: #1 tags after filtering in treatment: 8035745 INFO @ Mon, 29 Jun 2020 22:02:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:02:45: #1 finished! INFO @ Mon, 29 Jun 2020 22:02:45: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:02:45: #2 number of paired peaks: 29 WARNING @ Mon, 29 Jun 2020 22:02:45: Too few paired peaks (29) 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 22:02:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.10_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/SRX183887/SRX183887.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:02:47: 3000000 INFO @ Mon, 29 Jun 2020 22:02:53: 4000000 INFO @ Mon, 29 Jun 2020 22:02:58: 5000000 INFO @ Mon, 29 Jun 2020 22:03:03: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:03:09: 7000000 INFO @ Mon, 29 Jun 2020 22:03:14: 8000000 INFO @ Mon, 29 Jun 2020 22:03:14: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:03:14: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:03:14: #1 total tags in treatment: 8035745 INFO @ Mon, 29 Jun 2020 22:03:14: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:03:14: #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 22:03:14: #1 tags after filtering in treatment: 8035745 INFO @ Mon, 29 Jun 2020 22:03:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:03:14: #1 finished! INFO @ Mon, 29 Jun 2020 22:03:14: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:03:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:03:15: #2 number of paired peaks: 29 WARNING @ Mon, 29 Jun 2020 22:03:15: Too few paired peaks (29) 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 22:03:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.20_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/SRX183887/SRX183887.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX183887/SRX183887.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。