Job ID = 5790998 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,759,675 reads read : 11,519,350 reads written : 11,519,350 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: 00:02:35 5759675 reads; of these: 5759675 (100.00%) were paired; of these: 225365 (3.91%) aligned concordantly 0 times 4989399 (86.63%) aligned concordantly exactly 1 time 544911 (9.46%) aligned concordantly >1 times ---- 225365 pairs aligned concordantly 0 times; of these: 6535 (2.90%) aligned discordantly 1 time ---- 218830 pairs aligned 0 times concordantly or discordantly; of these: 437660 mates make up the pairs; of these: 398130 (90.97%) aligned 0 times 31115 (7.11%) aligned exactly 1 time 8415 (1.92%) aligned >1 times 96.54% overall alignment rate Time searching: 00:02:35 Overall time: 00:02:35 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_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] 318407 / 5535825 = 0.0575 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 08:15:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.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 08:15:39: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:39: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:15:43: 1000000 INFO @ Wed, 22 Apr 2020 08:15:47: 2000000 INFO @ Wed, 22 Apr 2020 08:15:51: 3000000 INFO @ Wed, 22 Apr 2020 08:15:55: 4000000 INFO @ Wed, 22 Apr 2020 08:15:59: 5000000 INFO @ Wed, 22 Apr 2020 08:16:03: 6000000 INFO @ Wed, 22 Apr 2020 08:16:07: 7000000 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 08:16:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.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 08:16:09: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:09: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:11: 8000000 INFO @ Wed, 22 Apr 2020 08:16:13: 1000000 INFO @ Wed, 22 Apr 2020 08:16:15: 9000000 INFO @ Wed, 22 Apr 2020 08:16:17: 2000000 INFO @ Wed, 22 Apr 2020 08:16:19: 10000000 INFO @ Wed, 22 Apr 2020 08:16:21: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:16:21: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:16:21: #1 total tags in treatment: 5215964 INFO @ Wed, 22 Apr 2020 08:16:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:21: #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 08:16:21: #1 tags after filtering in treatment: 4527525 INFO @ Wed, 22 Apr 2020 08:16:21: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Apr 2020 08:16:21: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:21: #2 number of paired peaks: 2 WARNING @ Wed, 22 Apr 2020 08:16:21: Too few paired peaks (2) 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 08:16:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.05_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/SRX5874497/SRX5874497.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:16:21: 3000000 INFO @ Wed, 22 Apr 2020 08:16:25: 4000000 INFO @ Wed, 22 Apr 2020 08:16:29: 5000000 INFO @ Wed, 22 Apr 2020 08:16:33: 6000000 BedGraph に変換中... INFO @ Wed, 22 Apr 2020 08:16:37: 7000000 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 08:16:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.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 08:16:39: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:39: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:41: 8000000 INFO @ Wed, 22 Apr 2020 08:16:43: 1000000 INFO @ Wed, 22 Apr 2020 08:16:45: 9000000 INFO @ Wed, 22 Apr 2020 08:16:48: 2000000 INFO @ Wed, 22 Apr 2020 08:16:49: 10000000 INFO @ Wed, 22 Apr 2020 08:16:51: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:16:51: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:16:51: #1 total tags in treatment: 5215964 INFO @ Wed, 22 Apr 2020 08:16:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:51: #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 08:16:51: #1 tags after filtering in treatment: 4527525 INFO @ Wed, 22 Apr 2020 08:16:51: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Apr 2020 08:16:51: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:52: 3000000 INFO @ Wed, 22 Apr 2020 08:16:52: #2 number of paired peaks: 2 WARNING @ Wed, 22 Apr 2020 08:16:52: Too few paired peaks (2) 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 08:16:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.10_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/SRX5874497/SRX5874497.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:16:56: 4000000 INFO @ Wed, 22 Apr 2020 08:17:00: 5000000 INFO @ Wed, 22 Apr 2020 08:17:04: 6000000 INFO @ Wed, 22 Apr 2020 08:17:08: 7000000 INFO @ Wed, 22 Apr 2020 08:17:12: 8000000 INFO @ Wed, 22 Apr 2020 08:17:16: 9000000 INFO @ Wed, 22 Apr 2020 08:17:20: 10000000 INFO @ Wed, 22 Apr 2020 08:17:21: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:17:21: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:17:21: #1 total tags in treatment: 5215964 INFO @ Wed, 22 Apr 2020 08:17:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:17:21: #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 08:17:22: #1 tags after filtering in treatment: 4527525 INFO @ Wed, 22 Apr 2020 08:17:22: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Apr 2020 08:17:22: #1 finished! INFO @ Wed, 22 Apr 2020 08:17:22: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:17:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:17:22: #2 number of paired peaks: 2 WARNING @ Wed, 22 Apr 2020 08:17:22: Too few paired peaks (2) 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 08:17:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.20_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/SRX5874497/SRX5874497.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874497/SRX5874497.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。