Job ID = 5791150 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,789,111 reads read : 17,578,222 reads written : 17,578,222 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: 00:11:20 8789111 reads; of these: 8789111 (100.00%) were paired; of these: 6560387 (74.64%) aligned concordantly 0 times 1401165 (15.94%) aligned concordantly exactly 1 time 827559 (9.42%) aligned concordantly >1 times ---- 6560387 pairs aligned concordantly 0 times; of these: 2258952 (34.43%) aligned discordantly 1 time ---- 4301435 pairs aligned 0 times concordantly or discordantly; of these: 8602870 mates make up the pairs; of these: 6424403 (74.68%) aligned 0 times 244353 (2.84%) aligned exactly 1 time 1934114 (22.48%) aligned >1 times 63.45% overall alignment rate Time searching: 00:11:20 Overall time: 00:11:20 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 12 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] 1065938 / 4342216 = 0.2455 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 09:10:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.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 09:10:06: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:10:06: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:10:13: 1000000 INFO @ Wed, 22 Apr 2020 09:10:22: 2000000 INFO @ Wed, 22 Apr 2020 09:10:29: 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 09:10:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.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 09:10:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:10:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:10:36: 4000000 INFO @ Wed, 22 Apr 2020 09:10:44: 1000000 INFO @ Wed, 22 Apr 2020 09:10:44: 5000000 INFO @ Wed, 22 Apr 2020 09:10:51: 2000000 INFO @ Wed, 22 Apr 2020 09:10:53: 6000000 INFO @ Wed, 22 Apr 2020 09:10:59: 3000000 INFO @ Wed, 22 Apr 2020 09:11:01: 7000000 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 09:11:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.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 09:11:06: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:11:06: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:11:07: 4000000 INFO @ Wed, 22 Apr 2020 09:11:08: 8000000 INFO @ Wed, 22 Apr 2020 09:11:14: 5000000 INFO @ Wed, 22 Apr 2020 09:11:15: 1000000 INFO @ Wed, 22 Apr 2020 09:11:16: 9000000 INFO @ Wed, 22 Apr 2020 09:11:16: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:11:16: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:11:16: #1 total tags in treatment: 1541770 INFO @ Wed, 22 Apr 2020 09:11:16: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:11:16: #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 09:11:16: #1 tags after filtering in treatment: 1131798 INFO @ Wed, 22 Apr 2020 09:11:16: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 22 Apr 2020 09:11:16: #1 finished! INFO @ Wed, 22 Apr 2020 09:11:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:11:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:11:16: #2 number of paired peaks: 55 WARNING @ Wed, 22 Apr 2020 09:11:16: Too few paired peaks (55) 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 09:11:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.05_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/SRX6614943/SRX6614943.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:11:22: 6000000 INFO @ Wed, 22 Apr 2020 09:11:23: 2000000 INFO @ Wed, 22 Apr 2020 09:11:30: 7000000 INFO @ Wed, 22 Apr 2020 09:11:32: 3000000 INFO @ Wed, 22 Apr 2020 09:11:37: 8000000 INFO @ Wed, 22 Apr 2020 09:11:41: 4000000 INFO @ Wed, 22 Apr 2020 09:11:45: 9000000 INFO @ Wed, 22 Apr 2020 09:11:45: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:11:45: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:11:45: #1 total tags in treatment: 1541770 INFO @ Wed, 22 Apr 2020 09:11:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:11:45: #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 09:11:45: #1 tags after filtering in treatment: 1131798 INFO @ Wed, 22 Apr 2020 09:11:45: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 22 Apr 2020 09:11:45: #1 finished! INFO @ Wed, 22 Apr 2020 09:11:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:11:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:11:45: #2 number of paired peaks: 55 WARNING @ Wed, 22 Apr 2020 09:11:45: Too few paired peaks (55) 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 09:11:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.10_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/SRX6614943/SRX6614943.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:11:50: 5000000 INFO @ Wed, 22 Apr 2020 09:11:58: 6000000 INFO @ Wed, 22 Apr 2020 09:12:07: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:12:16: 8000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:12:24: 9000000 INFO @ Wed, 22 Apr 2020 09:12:24: #1 tag size is determined as 151 bps INFO @ Wed, 22 Apr 2020 09:12:24: #1 tag size = 151 INFO @ Wed, 22 Apr 2020 09:12:24: #1 total tags in treatment: 1541770 INFO @ Wed, 22 Apr 2020 09:12:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:12:24: #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 09:12:24: #1 tags after filtering in treatment: 1131798 INFO @ Wed, 22 Apr 2020 09:12:24: #1 Redundant rate of treatment: 0.27 INFO @ Wed, 22 Apr 2020 09:12:24: #1 finished! INFO @ Wed, 22 Apr 2020 09:12:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:12:25: #2 number of paired peaks: 55 WARNING @ Wed, 22 Apr 2020 09:12:25: Too few paired peaks (55) 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 09:12:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.20_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/SRX6614943/SRX6614943.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614943/SRX6614943.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling