Job ID = 6528074 SRX = SRX3989975 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:15:35 prefetch.2.10.7: 1) Downloading 'SRR7059016'... 2020-06-29T14:15:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:16:57 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:16:57 prefetch.2.10.7: 'SRR7059016' is valid 2020-06-29T14:16:57 prefetch.2.10.7: 1) 'SRR7059016' was downloaded successfully 2020-06-29T14:16:57 prefetch.2.10.7: 'SRR7059016' has 0 unresolved dependencies Read 13253228 spots for SRR7059016/SRR7059016.sra Written 13253228 spots for SRR7059016/SRR7059016.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: 00:05:36 13253228 reads; of these: 13253228 (100.00%) were unpaired; of these: 2089192 (15.76%) aligned 0 times 7982059 (60.23%) aligned exactly 1 time 3181977 (24.01%) aligned >1 times 84.24% overall alignment rate Time searching: 00:05:36 Overall time: 00:05:36 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] 2107778 / 11164036 = 0.1888 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 23:29:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.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 23:29:45: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:29:45: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:29:51: 1000000 INFO @ Mon, 29 Jun 2020 23:29:56: 2000000 INFO @ Mon, 29 Jun 2020 23:30:02: 3000000 INFO @ Mon, 29 Jun 2020 23:30:08: 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 23:30:14: 5000000 INFO @ Mon, 29 Jun 2020 23:30:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.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 23:30:15: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:30:15: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:30:21: 6000000 INFO @ Mon, 29 Jun 2020 23:30:22: 1000000 INFO @ Mon, 29 Jun 2020 23:30:28: 7000000 INFO @ Mon, 29 Jun 2020 23:30:29: 2000000 INFO @ Mon, 29 Jun 2020 23:30:35: 8000000 INFO @ Mon, 29 Jun 2020 23:30:36: 3000000 INFO @ Mon, 29 Jun 2020 23:30:42: 9000000 INFO @ Mon, 29 Jun 2020 23:30:42: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 23:30:42: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 23:30:42: #1 total tags in treatment: 9056258 INFO @ Mon, 29 Jun 2020 23:30:42: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:30:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換中... INFO @ Mon, 29 Jun 2020 23:30:43: #1 tags after filtering in treatment: 9056258 INFO @ Mon, 29 Jun 2020 23:30:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:30:43: #1 finished! INFO @ Mon, 29 Jun 2020 23:30:43: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:30:43: #2 looking for paired plus/minus strand peaks... 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 23:30:43: 4000000 INFO @ Mon, 29 Jun 2020 23:30:43: #2 number of paired peaks: 17 WARNING @ Mon, 29 Jun 2020 23:30:43: Too few paired peaks (17) 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 23:30:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.05_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/SRX3989975/SRX3989975.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:30:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.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 23:30:45: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:30:45: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:30:50: 5000000 INFO @ Mon, 29 Jun 2020 23:30:53: 1000000 INFO @ Mon, 29 Jun 2020 23:30:58: 6000000 INFO @ Mon, 29 Jun 2020 23:31:02: 2000000 INFO @ Mon, 29 Jun 2020 23:31:05: 7000000 INFO @ Mon, 29 Jun 2020 23:31:10: 3000000 INFO @ Mon, 29 Jun 2020 23:31:13: 8000000 INFO @ Mon, 29 Jun 2020 23:31:19: 4000000 INFO @ Mon, 29 Jun 2020 23:31:21: 9000000 INFO @ Mon, 29 Jun 2020 23:31:21: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 23:31:21: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 23:31:21: #1 total tags in treatment: 9056258 INFO @ Mon, 29 Jun 2020 23:31:21: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:31:21: #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 23:31:21: #1 tags after filtering in treatment: 9056258 INFO @ Mon, 29 Jun 2020 23:31:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:31:21: #1 finished! INFO @ Mon, 29 Jun 2020 23:31:21: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:31:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:31:22: #2 number of paired peaks: 17 WARNING @ Mon, 29 Jun 2020 23:31:22: Too few paired peaks (17) 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 23:31:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.10_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/SRX3989975/SRX3989975.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:31:27: 5000000 INFO @ Mon, 29 Jun 2020 23:31:35: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:31:42: 7000000 INFO @ Mon, 29 Jun 2020 23:31:50: 8000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:31:57: 9000000 INFO @ Mon, 29 Jun 2020 23:31:58: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 23:31:58: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 23:31:58: #1 total tags in treatment: 9056258 INFO @ Mon, 29 Jun 2020 23:31:58: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:31:58: #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 23:31:58: #1 tags after filtering in treatment: 9056258 INFO @ Mon, 29 Jun 2020 23:31:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:31:58: #1 finished! INFO @ Mon, 29 Jun 2020 23:31:58: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:31:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:31:59: #2 number of paired peaks: 17 WARNING @ Mon, 29 Jun 2020 23:31:59: Too few paired peaks (17) 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 23:31:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.20_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/SRX3989975/SRX3989975.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/dm3/SRX3989975/SRX3989975.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling