Job ID = 5791060 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,498,712 reads read : 10,997,424 reads written : 10,997,424 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: 00:01:51 5498712 reads; of these: 5498712 (100.00%) were paired; of these: 1881654 (34.22%) aligned concordantly 0 times 3281685 (59.68%) aligned concordantly exactly 1 time 335373 (6.10%) aligned concordantly >1 times ---- 1881654 pairs aligned concordantly 0 times; of these: 46519 (2.47%) aligned discordantly 1 time ---- 1835135 pairs aligned 0 times concordantly or discordantly; of these: 3670270 mates make up the pairs; of these: 2565890 (69.91%) aligned 0 times 991318 (27.01%) aligned exactly 1 time 113062 (3.08%) aligned >1 times 76.67% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 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] 816803 / 3654068 = 0.2235 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 08:28:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.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 08:28:48: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:28:48: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:28:53: 1000000 INFO @ Wed, 22 Apr 2020 08:28:57: 2000000 INFO @ Wed, 22 Apr 2020 08:29:02: 3000000 INFO @ Wed, 22 Apr 2020 08:29:07: 4000000 INFO @ Wed, 22 Apr 2020 08:29:11: 5000000 INFO @ Wed, 22 Apr 2020 08:29:16: 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 08:29:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.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 08:29:18: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:29:18: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:29:20: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 08:29:20: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 08:29:20: #1 total tags in treatment: 2807028 INFO @ Wed, 22 Apr 2020 08:29:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:29:20: #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 08:29:20: #1 tags after filtering in treatment: 2434049 INFO @ Wed, 22 Apr 2020 08:29:20: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Apr 2020 08:29:20: #1 finished! INFO @ Wed, 22 Apr 2020 08:29:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:29:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:29:20: #2 number of paired peaks: 35 WARNING @ Wed, 22 Apr 2020 08:29:20: Too few paired peaks (35) 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 08:29:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.05_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/SRX5883284/SRX5883284.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:29:23: 1000000 INFO @ Wed, 22 Apr 2020 08:29:27: 2000000 INFO @ Wed, 22 Apr 2020 08:29:32: 3000000 INFO @ Wed, 22 Apr 2020 08:29:37: 4000000 INFO @ Wed, 22 Apr 2020 08:29:41: 5000000 INFO @ Wed, 22 Apr 2020 08:29:46: 6000000 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 08:29:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.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 08:29:48: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:29:48: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:29:50: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 08:29:50: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 08:29:50: #1 total tags in treatment: 2807028 INFO @ Wed, 22 Apr 2020 08:29:50: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:29:50: #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 08:29:50: #1 tags after filtering in treatment: 2434049 INFO @ Wed, 22 Apr 2020 08:29:50: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Apr 2020 08:29:50: #1 finished! INFO @ Wed, 22 Apr 2020 08:29:50: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:29:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:29:50: #2 number of paired peaks: 35 WARNING @ Wed, 22 Apr 2020 08:29:50: Too few paired peaks (35) 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 08:29:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.10_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/SRX5883284/SRX5883284.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:29:53: 1000000 INFO @ Wed, 22 Apr 2020 08:29:58: 2000000 INFO @ Wed, 22 Apr 2020 08:30:02: 3000000 INFO @ Wed, 22 Apr 2020 08:30:07: 4000000 INFO @ Wed, 22 Apr 2020 08:30:12: 5000000 INFO @ Wed, 22 Apr 2020 08:30:16: 6000000 INFO @ Wed, 22 Apr 2020 08:30:20: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 08:30:20: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 08:30:20: #1 total tags in treatment: 2807028 INFO @ Wed, 22 Apr 2020 08:30:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:30:20: #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 08:30:20: #1 tags after filtering in treatment: 2434049 INFO @ Wed, 22 Apr 2020 08:30:20: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Apr 2020 08:30:20: #1 finished! INFO @ Wed, 22 Apr 2020 08:30:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:30:20: #2 number of paired peaks: 35 WARNING @ Wed, 22 Apr 2020 08:30:20: Too few paired peaks (35) 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 08:30:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.20_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/SRX5883284/SRX5883284.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883284/SRX5883284.20_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。