Job ID = 5791125 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,963,731 reads read : 11,927,462 reads written : 11,927,462 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: 00:02:15 5963731 reads; of these: 5963731 (100.00%) were paired; of these: 761182 (12.76%) aligned concordantly 0 times 3580916 (60.04%) aligned concordantly exactly 1 time 1621633 (27.19%) aligned concordantly >1 times ---- 761182 pairs aligned concordantly 0 times; of these: 1017 (0.13%) aligned discordantly 1 time ---- 760165 pairs aligned 0 times concordantly or discordantly; of these: 1520330 mates make up the pairs; of these: 1495460 (98.36%) aligned 0 times 15436 (1.02%) aligned exactly 1 time 9434 (0.62%) aligned >1 times 87.46% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 951990 / 5201731 = 0.1830 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 08:39:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.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 08:39:40: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:39:40: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:39:45: 1000000 INFO @ Wed, 22 Apr 2020 08:39:49: 2000000 INFO @ Wed, 22 Apr 2020 08:39:54: 3000000 INFO @ Wed, 22 Apr 2020 08:39:59: 4000000 INFO @ Wed, 22 Apr 2020 08:40:03: 5000000 INFO @ Wed, 22 Apr 2020 08:40:08: 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 08:40:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.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 08:40:10: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:40:10: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:40:12: 7000000 INFO @ Wed, 22 Apr 2020 08:40:15: 1000000 INFO @ Wed, 22 Apr 2020 08:40:17: 8000000 INFO @ Wed, 22 Apr 2020 08:40:20: 2000000 INFO @ Wed, 22 Apr 2020 08:40:20: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 08:40:20: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 08:40:20: #1 total tags in treatment: 4250571 INFO @ Wed, 22 Apr 2020 08:40:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:40:20: #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 08:40:20: #1 tags after filtering in treatment: 2849654 INFO @ Wed, 22 Apr 2020 08:40:20: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 08:40:20: #1 finished! INFO @ Wed, 22 Apr 2020 08:40:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:40:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:40:20: #2 number of paired peaks: 29 WARNING @ Wed, 22 Apr 2020 08:40:20: Too few paired peaks (29) 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 08:40:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.05_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/SRX6614921/SRX6614921.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:40:24: 3000000 INFO @ Wed, 22 Apr 2020 08:40:29: 4000000 INFO @ Wed, 22 Apr 2020 08:40:34: 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 08:40:38: 6000000 INFO @ Wed, 22 Apr 2020 08:40:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.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 08:40:40: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:40:40: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:40:43: 7000000 INFO @ Wed, 22 Apr 2020 08:40:45: 1000000 INFO @ Wed, 22 Apr 2020 08:40:48: 8000000 INFO @ Wed, 22 Apr 2020 08:40:50: 2000000 INFO @ Wed, 22 Apr 2020 08:40:51: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 08:40:51: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 08:40:51: #1 total tags in treatment: 4250571 INFO @ Wed, 22 Apr 2020 08:40:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:40:51: #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 08:40:51: #1 tags after filtering in treatment: 2849654 INFO @ Wed, 22 Apr 2020 08:40:51: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 08:40:51: #1 finished! INFO @ Wed, 22 Apr 2020 08:40:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:40:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:40:51: #2 number of paired peaks: 29 WARNING @ Wed, 22 Apr 2020 08:40:51: Too few paired peaks (29) 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 08:40:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.10_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/SRX6614921/SRX6614921.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:40:55: 3000000 INFO @ Wed, 22 Apr 2020 08:41:00: 4000000 INFO @ Wed, 22 Apr 2020 08:41:04: 5000000 INFO @ Wed, 22 Apr 2020 08:41:09: 6000000 INFO @ Wed, 22 Apr 2020 08:41:14: 7000000 INFO @ Wed, 22 Apr 2020 08:41:19: 8000000 INFO @ Wed, 22 Apr 2020 08:41:21: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 08:41:21: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 08:41:21: #1 total tags in treatment: 4250571 INFO @ Wed, 22 Apr 2020 08:41:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:41:21: #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 08:41:21: #1 tags after filtering in treatment: 2849654 INFO @ Wed, 22 Apr 2020 08:41:21: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 08:41:21: #1 finished! INFO @ Wed, 22 Apr 2020 08:41:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:41:21: #2 number of paired peaks: 29 WARNING @ Wed, 22 Apr 2020 08:41:21: Too few paired peaks (29) 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 08:41:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.20_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/SRX6614921/SRX6614921.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614921/SRX6614921.20_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。