Job ID = 5791139 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,924,269 reads read : 15,848,538 reads written : 15,848,538 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: 00:06:17 7924269 reads; of these: 7924269 (100.00%) were paired; of these: 2470340 (31.17%) aligned concordantly 0 times 3867667 (48.81%) aligned concordantly exactly 1 time 1586262 (20.02%) aligned concordantly >1 times ---- 2470340 pairs aligned concordantly 0 times; of these: 294993 (11.94%) aligned discordantly 1 time ---- 2175347 pairs aligned 0 times concordantly or discordantly; of these: 4350694 mates make up the pairs; of these: 3519623 (80.90%) aligned 0 times 90186 (2.07%) aligned exactly 1 time 740885 (17.03%) aligned >1 times 77.79% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 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] 1795974 / 5710924 = 0.3145 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 08:54:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.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 08:54:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:54:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:54:56: 1000000 INFO @ Wed, 22 Apr 2020 08:55:02: 2000000 INFO @ Wed, 22 Apr 2020 08:55:08: 3000000 INFO @ Wed, 22 Apr 2020 08:55:14: 4000000 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 08:55:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.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 08:55:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:55:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:55:23: 5000000 INFO @ Wed, 22 Apr 2020 08:55:29: 1000000 INFO @ Wed, 22 Apr 2020 08:55:32: 6000000 INFO @ Wed, 22 Apr 2020 08:55:38: 2000000 INFO @ Wed, 22 Apr 2020 08:55:41: 7000000 INFO @ Wed, 22 Apr 2020 08:55:47: 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 08:55:49: 8000000 INFO @ Wed, 22 Apr 2020 08:55:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.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 08:55:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:55:49: #1 read treatment tags... 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: 3704317 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: 2499922 INFO @ Wed, 22 Apr 2020 08:55:55: #1 Redundant rate of treatment: 0.33 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: 30 WARNING @ Wed, 22 Apr 2020 08:55:55: Too few paired peaks (30) 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/SRX6614932/SRX6614932.05_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/SRX6614932/SRX6614932.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:55:56: 4000000 INFO @ Wed, 22 Apr 2020 08:55:59: 1000000 INFO @ Wed, 22 Apr 2020 08:56:06: 5000000 INFO @ Wed, 22 Apr 2020 08:56:08: 2000000 INFO @ Wed, 22 Apr 2020 08:56:15: 6000000 INFO @ Wed, 22 Apr 2020 08:56:17: 3000000 INFO @ Wed, 22 Apr 2020 08:56:24: 7000000 INFO @ Wed, 22 Apr 2020 08:56:27: 4000000 INFO @ Wed, 22 Apr 2020 08:56:33: 8000000 INFO @ Wed, 22 Apr 2020 08:56:36: 5000000 INFO @ Wed, 22 Apr 2020 08:56:40: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 08:56:40: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 08:56:40: #1 total tags in treatment: 3704317 INFO @ Wed, 22 Apr 2020 08:56:40: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:56:40: #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 08:56:40: #1 tags after filtering in treatment: 2499922 INFO @ Wed, 22 Apr 2020 08:56:40: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 08:56:40: #1 finished! INFO @ Wed, 22 Apr 2020 08:56:40: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:56:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:56:40: #2 number of paired peaks: 30 WARNING @ Wed, 22 Apr 2020 08:56:40: Too few paired peaks (30) 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 08:56:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.10_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/SRX6614932/SRX6614932.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:56:45: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:56:54: 7000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 08:57:02: 8000000 INFO @ Wed, 22 Apr 2020 08:57:09: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 08:57:09: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 08:57:09: #1 total tags in treatment: 3704317 INFO @ Wed, 22 Apr 2020 08:57:09: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:57:09: #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 08:57:09: #1 tags after filtering in treatment: 2499922 INFO @ Wed, 22 Apr 2020 08:57:09: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Apr 2020 08:57:09: #1 finished! INFO @ Wed, 22 Apr 2020 08:57:09: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:57:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:57:09: #2 number of paired peaks: 30 WARNING @ Wed, 22 Apr 2020 08:57:09: Too few paired peaks (30) 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 08:57:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.20_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/SRX6614932/SRX6614932.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614932/SRX6614932.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling