Job ID = 5791136 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,425,657 reads read : 16,851,314 reads written : 16,851,314 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: 00:07:00 8425657 reads; of these: 8425657 (100.00%) were paired; of these: 1889024 (22.42%) aligned concordantly 0 times 4221633 (50.10%) aligned concordantly exactly 1 time 2315000 (27.48%) aligned concordantly >1 times ---- 1889024 pairs aligned concordantly 0 times; of these: 453696 (24.02%) aligned discordantly 1 time ---- 1435328 pairs aligned 0 times concordantly or discordantly; of these: 2870656 mates make up the pairs; of these: 2284948 (79.60%) aligned 0 times 96233 (3.35%) aligned exactly 1 time 489475 (17.05%) aligned >1 times 86.44% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 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] 2322371 / 6939870 = 0.3346 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 08:54:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.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 08:54:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:54:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:54:31: 1000000 INFO @ Wed, 22 Apr 2020 08:54:40: 2000000 INFO @ Wed, 22 Apr 2020 08:54:48: 3000000 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 08:54:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.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 08:54:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:54:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:54:57: 4000000 INFO @ Wed, 22 Apr 2020 08:55:02: 1000000 INFO @ Wed, 22 Apr 2020 08:55:07: 5000000 INFO @ Wed, 22 Apr 2020 08:55:11: 2000000 INFO @ Wed, 22 Apr 2020 08:55:16: 6000000 INFO @ Wed, 22 Apr 2020 08:55:20: 3000000 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 08:55:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.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 08:55:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:55:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:55:25: 7000000 INFO @ Wed, 22 Apr 2020 08:55:30: 4000000 INFO @ Wed, 22 Apr 2020 08:55:34: 1000000 INFO @ Wed, 22 Apr 2020 08:55:36: 8000000 INFO @ Wed, 22 Apr 2020 08:55:39: 5000000 INFO @ Wed, 22 Apr 2020 08:55:44: 2000000 INFO @ Wed, 22 Apr 2020 08:55:46: 9000000 INFO @ Wed, 22 Apr 2020 08:55:48: 6000000 INFO @ Wed, 22 Apr 2020 08:55:54: 3000000 INFO @ Wed, 22 Apr 2020 08:55:55: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 08:55:55: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 08:55:55: #1 total tags in treatment: 4280371 INFO @ Wed, 22 Apr 2020 08:55:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:55:55: #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 08:55:55: #1 tags after filtering in treatment: 2732761 INFO @ Wed, 22 Apr 2020 08:55:55: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Apr 2020 08:55:55: #1 finished! INFO @ Wed, 22 Apr 2020 08:55:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:55:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:55:55: #2 number of paired peaks: 28 WARNING @ Wed, 22 Apr 2020 08:55:55: Too few paired peaks (28) 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 08:55:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.05_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/SRX6614929/SRX6614929.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:55:57: 7000000 INFO @ Wed, 22 Apr 2020 08:56:03: 4000000 INFO @ Wed, 22 Apr 2020 08:56:06: 8000000 INFO @ Wed, 22 Apr 2020 08:56:12: 5000000 INFO @ Wed, 22 Apr 2020 08:56:15: 9000000 INFO @ Wed, 22 Apr 2020 08:56:21: 6000000 INFO @ Wed, 22 Apr 2020 08:56:23: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 08:56:23: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 08:56:23: #1 total tags in treatment: 4280371 INFO @ Wed, 22 Apr 2020 08:56:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:56:23: #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 08:56:23: #1 tags after filtering in treatment: 2732761 INFO @ Wed, 22 Apr 2020 08:56:23: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Apr 2020 08:56:23: #1 finished! INFO @ Wed, 22 Apr 2020 08:56:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:56:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:56:23: #2 number of paired peaks: 28 WARNING @ Wed, 22 Apr 2020 08:56:23: Too few paired peaks (28) 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 08:56:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.10_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/SRX6614929/SRX6614929.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.10_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 08:56:29: 7000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 08:56:37: 8000000 INFO @ Wed, 22 Apr 2020 08:56:45: 9000000 INFO @ Wed, 22 Apr 2020 08:56:52: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 08:56:52: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 08:56:52: #1 total tags in treatment: 4280371 INFO @ Wed, 22 Apr 2020 08:56:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:56:52: #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 08:56:52: #1 tags after filtering in treatment: 2732761 INFO @ Wed, 22 Apr 2020 08:56:52: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Apr 2020 08:56:52: #1 finished! INFO @ Wed, 22 Apr 2020 08:56:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:56:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:56:52: #2 number of paired peaks: 28 WARNING @ Wed, 22 Apr 2020 08:56:52: Too few paired peaks (28) 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 08:56:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.20_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/SRX6614929/SRX6614929.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614929/SRX6614929.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling