Job ID = 5791660 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 28,277,368 reads read : 56,554,736 reads written : 56,554,736 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:19:38 28277368 reads; of these: 28277368 (100.00%) were paired; of these: 7806632 (27.61%) aligned concordantly 0 times 16116427 (56.99%) aligned concordantly exactly 1 time 4354309 (15.40%) aligned concordantly >1 times ---- 7806632 pairs aligned concordantly 0 times; of these: 15096 (0.19%) aligned discordantly 1 time ---- 7791536 pairs aligned 0 times concordantly or discordantly; of these: 15583072 mates make up the pairs; of these: 15286413 (98.10%) aligned 0 times 188946 (1.21%) aligned exactly 1 time 107713 (0.69%) aligned >1 times 72.97% overall alignment rate Time searching: 00:19:38 Overall time: 00:19:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 20 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 8841406 / 20479727 = 0.4317 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 @ Wed, 22 Apr 2020 11:01:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 11:01:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:01:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:01:59: 1000000 INFO @ Wed, 22 Apr 2020 11:02:04: 2000000 INFO @ Wed, 22 Apr 2020 11:02:08: 3000000 INFO @ Wed, 22 Apr 2020 11:02:12: 4000000 INFO @ Wed, 22 Apr 2020 11:02:17: 5000000 INFO @ Wed, 22 Apr 2020 11:02:21: 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 @ Wed, 22 Apr 2020 11:02:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 11:02:25: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:02:25: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:02:25: 7000000 INFO @ Wed, 22 Apr 2020 11:02:30: 1000000 INFO @ Wed, 22 Apr 2020 11:02:30: 8000000 INFO @ Wed, 22 Apr 2020 11:02:34: 2000000 INFO @ Wed, 22 Apr 2020 11:02:34: 9000000 INFO @ Wed, 22 Apr 2020 11:02:38: 3000000 INFO @ Wed, 22 Apr 2020 11:02:39: 10000000 INFO @ Wed, 22 Apr 2020 11:02:43: 4000000 INFO @ Wed, 22 Apr 2020 11:02:43: 11000000 INFO @ Wed, 22 Apr 2020 11:02:47: 5000000 INFO @ Wed, 22 Apr 2020 11:02:47: 12000000 INFO @ Wed, 22 Apr 2020 11:02:52: 6000000 INFO @ Wed, 22 Apr 2020 11:02:52: 13000000 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 @ Wed, 22 Apr 2020 11:02:56: 7000000 INFO @ Wed, 22 Apr 2020 11:02:56: 14000000 INFO @ Wed, 22 Apr 2020 11:02:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 11:02:56: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:02:56: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:03:01: 8000000 INFO @ Wed, 22 Apr 2020 11:03:01: 15000000 INFO @ Wed, 22 Apr 2020 11:03:01: 1000000 INFO @ Wed, 22 Apr 2020 11:03:05: 16000000 INFO @ Wed, 22 Apr 2020 11:03:05: 9000000 INFO @ Wed, 22 Apr 2020 11:03:05: 2000000 INFO @ Wed, 22 Apr 2020 11:03:09: 17000000 INFO @ Wed, 22 Apr 2020 11:03:09: 3000000 INFO @ Wed, 22 Apr 2020 11:03:09: 10000000 INFO @ Wed, 22 Apr 2020 11:03:14: 18000000 INFO @ Wed, 22 Apr 2020 11:03:14: 4000000 INFO @ Wed, 22 Apr 2020 11:03:14: 11000000 INFO @ Wed, 22 Apr 2020 11:03:18: 19000000 INFO @ Wed, 22 Apr 2020 11:03:18: 5000000 INFO @ Wed, 22 Apr 2020 11:03:18: 12000000 INFO @ Wed, 22 Apr 2020 11:03:23: 20000000 INFO @ Wed, 22 Apr 2020 11:03:23: 13000000 INFO @ Wed, 22 Apr 2020 11:03:23: 6000000 INFO @ Wed, 22 Apr 2020 11:03:27: 21000000 INFO @ Wed, 22 Apr 2020 11:03:27: 14000000 INFO @ Wed, 22 Apr 2020 11:03:27: 7000000 INFO @ Wed, 22 Apr 2020 11:03:31: 15000000 INFO @ Wed, 22 Apr 2020 11:03:31: 22000000 INFO @ Wed, 22 Apr 2020 11:03:31: 8000000 INFO @ Wed, 22 Apr 2020 11:03:36: 16000000 INFO @ Wed, 22 Apr 2020 11:03:36: 23000000 INFO @ Wed, 22 Apr 2020 11:03:36: 9000000 INFO @ Wed, 22 Apr 2020 11:03:39: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 11:03:39: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 11:03:39: #1 total tags in treatment: 11632015 INFO @ Wed, 22 Apr 2020 11:03:39: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:03:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 11:03:39: #1 tags after filtering in treatment: 5175273 INFO @ Wed, 22 Apr 2020 11:03:39: #1 Redundant rate of treatment: 0.56 INFO @ Wed, 22 Apr 2020 11:03:39: #1 finished! INFO @ Wed, 22 Apr 2020 11:03:39: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:03:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:03:39: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:03:39: Too few paired peaks (0) 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 @ Wed, 22 Apr 2020 11:03:39: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 11:03:40: 17000000 INFO @ Wed, 22 Apr 2020 11:03:40: 10000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.05_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/sacCer3/SRX7409623/SRX7409623.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:03:44: 18000000 INFO @ Wed, 22 Apr 2020 11:03:45: 11000000 INFO @ Wed, 22 Apr 2020 11:03:49: 19000000 INFO @ Wed, 22 Apr 2020 11:03:49: 12000000 INFO @ Wed, 22 Apr 2020 11:03:53: 20000000 INFO @ Wed, 22 Apr 2020 11:03:53: 13000000 INFO @ Wed, 22 Apr 2020 11:03:57: 21000000 INFO @ Wed, 22 Apr 2020 11:03:58: 14000000 INFO @ Wed, 22 Apr 2020 11:04:02: 22000000 INFO @ Wed, 22 Apr 2020 11:04:02: 15000000 INFO @ Wed, 22 Apr 2020 11:04:06: 23000000 INFO @ Wed, 22 Apr 2020 11:04:06: 16000000 INFO @ Wed, 22 Apr 2020 11:04:09: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 11:04:09: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 11:04:09: #1 total tags in treatment: 11632015 INFO @ Wed, 22 Apr 2020 11:04:09: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:04:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 11:04:09: #1 tags after filtering in treatment: 5175273 INFO @ Wed, 22 Apr 2020 11:04:09: #1 Redundant rate of treatment: 0.56 INFO @ Wed, 22 Apr 2020 11:04:09: #1 finished! INFO @ Wed, 22 Apr 2020 11:04:09: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:04:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:04:09: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:04:09: Too few paired peaks (0) 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 @ Wed, 22 Apr 2020 11:04:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.10_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/sacCer3/SRX7409623/SRX7409623.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:04:11: 17000000 INFO @ Wed, 22 Apr 2020 11:04:15: 18000000 INFO @ Wed, 22 Apr 2020 11:04:19: 19000000 INFO @ Wed, 22 Apr 2020 11:04:23: 20000000 INFO @ Wed, 22 Apr 2020 11:04:28: 21000000 INFO @ Wed, 22 Apr 2020 11:04:32: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:04:36: 23000000 INFO @ Wed, 22 Apr 2020 11:04:39: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 11:04:39: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 11:04:39: #1 total tags in treatment: 11632015 INFO @ Wed, 22 Apr 2020 11:04:39: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:04:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 11:04:39: #1 tags after filtering in treatment: 5175273 INFO @ Wed, 22 Apr 2020 11:04:39: #1 Redundant rate of treatment: 0.56 INFO @ Wed, 22 Apr 2020 11:04:39: #1 finished! INFO @ Wed, 22 Apr 2020 11:04:39: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:04:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:04:39: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:04:39: Too few paired peaks (0) 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 @ Wed, 22 Apr 2020 11:04:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.20_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/sacCer3/SRX7409623/SRX7409623.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409623/SRX7409623.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。