Job ID = 6527706 SRX = SRX2325649 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:11:49 prefetch.2.10.7: 1) Downloading 'SRR4896337'... 2020-06-29T13:11:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:16:34 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:16:34 prefetch.2.10.7: 1) 'SRR4896337' was downloaded successfully 2020-06-29T13:16:34 prefetch.2.10.7: 'SRR4896337' has 0 unresolved dependencies Read 53329806 spots for SRR4896337/SRR4896337.sra Written 53329806 spots for SRR4896337/SRR4896337.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: 00:11:22 53329806 reads; of these: 53329806 (100.00%) were unpaired; of these: 40380021 (75.72%) aligned 0 times 9983136 (18.72%) aligned exactly 1 time 2966649 (5.56%) aligned >1 times 24.28% overall alignment rate Time searching: 00:11:22 Overall time: 00:11:22 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 8 files... [bam_rmdupse_core] 5598886 / 12949785 = 0.4324 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 22:52:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.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 22:52:48: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:52:48: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:52:54: 1000000 INFO @ Mon, 29 Jun 2020 22:53:01: 2000000 INFO @ Mon, 29 Jun 2020 22:53:08: 3000000 INFO @ Mon, 29 Jun 2020 22:53:15: 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 22:53:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.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 22:53:18: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:53:18: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:53:22: 5000000 INFO @ Mon, 29 Jun 2020 22:53:25: 1000000 INFO @ Mon, 29 Jun 2020 22:53:30: 6000000 INFO @ Mon, 29 Jun 2020 22:53:32: 2000000 INFO @ Mon, 29 Jun 2020 22:53:38: 7000000 INFO @ Mon, 29 Jun 2020 22:53:39: 3000000 INFO @ Mon, 29 Jun 2020 22:53:40: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 22:53:40: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 22:53:40: #1 total tags in treatment: 7350899 INFO @ Mon, 29 Jun 2020 22:53:40: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:53:40: #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 22:53:40: #1 tags after filtering in treatment: 7350899 INFO @ Mon, 29 Jun 2020 22:53:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:53:40: #1 finished! INFO @ Mon, 29 Jun 2020 22:53:40: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:53:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:53:41: #2 number of paired peaks: 91 WARNING @ Mon, 29 Jun 2020 22:53:41: Too few paired peaks (91) 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 22:53:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.05_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/SRX2325649/SRX2325649.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:53:45: 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 22:53:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.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 22:53:48: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:53:48: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:53:52: 5000000 INFO @ Mon, 29 Jun 2020 22:53:55: 1000000 INFO @ Mon, 29 Jun 2020 22:53:59: 6000000 INFO @ Mon, 29 Jun 2020 22:54:03: 2000000 INFO @ Mon, 29 Jun 2020 22:54:07: 7000000 INFO @ Mon, 29 Jun 2020 22:54:09: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 22:54:09: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 22:54:09: #1 total tags in treatment: 7350899 INFO @ Mon, 29 Jun 2020 22:54:09: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:54:09: #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 22:54:09: #1 tags after filtering in treatment: 7350899 INFO @ Mon, 29 Jun 2020 22:54:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:54:09: #1 finished! INFO @ Mon, 29 Jun 2020 22:54:09: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:54:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:54:10: #2 number of paired peaks: 91 WARNING @ Mon, 29 Jun 2020 22:54:10: Too few paired peaks (91) 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 22:54:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.10_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/SRX2325649/SRX2325649.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:54:10: 3000000 INFO @ Mon, 29 Jun 2020 22:54:17: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:54:24: 5000000 INFO @ Mon, 29 Jun 2020 22:54:32: 6000000 INFO @ Mon, 29 Jun 2020 22:54:39: 7000000 INFO @ Mon, 29 Jun 2020 22:54:41: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 22:54:41: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 22:54:41: #1 total tags in treatment: 7350899 INFO @ Mon, 29 Jun 2020 22:54:41: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:54:41: #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 22:54:41: #1 tags after filtering in treatment: 7350899 INFO @ Mon, 29 Jun 2020 22:54:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:54:41: #1 finished! INFO @ Mon, 29 Jun 2020 22:54:41: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:54:41: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:54:42: #2 number of paired peaks: 91 WARNING @ Mon, 29 Jun 2020 22:54:42: Too few paired peaks (91) 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 22:54:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.20_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/SRX2325649/SRX2325649.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX2325649/SRX2325649.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling