Job ID = 5791162 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,325,569 reads read : 12,651,138 reads written : 12,651,138 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: 00:07:29 6325569 reads; of these: 6325569 (100.00%) were paired; of these: 4512893 (71.34%) aligned concordantly 0 times 1479130 (23.38%) aligned concordantly exactly 1 time 333546 (5.27%) aligned concordantly >1 times ---- 4512893 pairs aligned concordantly 0 times; of these: 2027955 (44.94%) aligned discordantly 1 time ---- 2484938 pairs aligned 0 times concordantly or discordantly; of these: 4969876 mates make up the pairs; of these: 4088815 (82.27%) aligned 0 times 170009 (3.42%) aligned exactly 1 time 711052 (14.31%) aligned >1 times 67.68% overall alignment rate Time searching: 00:07:29 Overall time: 00:07:29 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 8 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] 597721 / 3727870 = 0.1603 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 09:01:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.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 09:01:58: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:01:58: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:02:08: 1000000 INFO @ Wed, 22 Apr 2020 09:02:19: 2000000 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 09:02:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.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 09:02:28: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:02:28: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:02:29: 3000000 INFO @ Wed, 22 Apr 2020 09:02:40: 1000000 INFO @ Wed, 22 Apr 2020 09:02:41: 4000000 INFO @ Wed, 22 Apr 2020 09:02:51: 2000000 INFO @ Wed, 22 Apr 2020 09:02:52: 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 @ Wed, 22 Apr 2020 09:02:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.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 09:02:58: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:02:58: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:03:03: 3000000 INFO @ Wed, 22 Apr 2020 09:03:03: 6000000 INFO @ Wed, 22 Apr 2020 09:03:08: 1000000 INFO @ Wed, 22 Apr 2020 09:03:15: 4000000 INFO @ Wed, 22 Apr 2020 09:03:16: 7000000 INFO @ Wed, 22 Apr 2020 09:03:19: 2000000 INFO @ Wed, 22 Apr 2020 09:03:20: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:03:20: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:03:20: #1 total tags in treatment: 1496365 INFO @ Wed, 22 Apr 2020 09:03:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:03:20: #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 09:03:20: #1 tags after filtering in treatment: 1209861 INFO @ Wed, 22 Apr 2020 09:03:20: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 09:03:20: #1 finished! INFO @ Wed, 22 Apr 2020 09:03:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:03:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:03:20: #2 number of paired peaks: 20 WARNING @ Wed, 22 Apr 2020 09:03:20: Too few paired peaks (20) 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 09:03:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.05_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/SRX6614956/SRX6614956.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:03:27: 5000000 INFO @ Wed, 22 Apr 2020 09:03:29: 3000000 INFO @ Wed, 22 Apr 2020 09:03:39: 4000000 INFO @ Wed, 22 Apr 2020 09:03:39: 6000000 INFO @ Wed, 22 Apr 2020 09:03:49: 5000000 INFO @ Wed, 22 Apr 2020 09:03:51: 7000000 INFO @ Wed, 22 Apr 2020 09:03:55: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:03:55: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:03:55: #1 total tags in treatment: 1496365 INFO @ Wed, 22 Apr 2020 09:03:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:03:55: #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 09:03:55: #1 tags after filtering in treatment: 1209861 INFO @ Wed, 22 Apr 2020 09:03:55: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 09:03:55: #1 finished! INFO @ Wed, 22 Apr 2020 09:03:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:03:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:03:56: #2 number of paired peaks: 20 WARNING @ Wed, 22 Apr 2020 09:03:56: Too few paired peaks (20) 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 09:03:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 12 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:03:59: 6000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:04:07: 7000000 INFO @ Wed, 22 Apr 2020 09:04:10: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:04:10: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:04:10: #1 total tags in treatment: 1496365 INFO @ Wed, 22 Apr 2020 09:04:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:04:10: #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 09:04:10: #1 tags after filtering in treatment: 1209861 INFO @ Wed, 22 Apr 2020 09:04:10: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 09:04:10: #1 finished! INFO @ Wed, 22 Apr 2020 09:04:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:04:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:04:10: #2 number of paired peaks: 20 WARNING @ Wed, 22 Apr 2020 09:04:10: Too few paired peaks (20) 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 09:04:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.20_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/sacCer3/SRX6614956/SRX6614956.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614956/SRX6614956.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling