Job ID = 5791823 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,801,695 reads read : 23,603,390 reads written : 23,603,390 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: 00:07:35 11801695 reads; of these: 11801695 (100.00%) were paired; of these: 2753278 (23.33%) aligned concordantly 0 times 7803618 (66.12%) aligned concordantly exactly 1 time 1244799 (10.55%) aligned concordantly >1 times ---- 2753278 pairs aligned concordantly 0 times; of these: 919384 (33.39%) aligned discordantly 1 time ---- 1833894 pairs aligned 0 times concordantly or discordantly; of these: 3667788 mates make up the pairs; of these: 3152448 (85.95%) aligned 0 times 208517 (5.69%) aligned exactly 1 time 306823 (8.37%) aligned >1 times 86.64% overall alignment rate Time searching: 00:07:35 Overall time: 00:07:35 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_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] 2786434 / 9899926 = 0.2815 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 11:08:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.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 11:08:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:08:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:08:42: 1000000 INFO @ Wed, 22 Apr 2020 11:08:47: 2000000 INFO @ Wed, 22 Apr 2020 11:08:53: 3000000 INFO @ Wed, 22 Apr 2020 11:08:59: 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 11:09:05: 5000000 INFO @ Wed, 22 Apr 2020 11:09:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.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 11:09:06: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:09:06: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:09:10: 6000000 INFO @ Wed, 22 Apr 2020 11:09:12: 1000000 INFO @ Wed, 22 Apr 2020 11:09:16: 7000000 INFO @ Wed, 22 Apr 2020 11:09:17: 2000000 INFO @ Wed, 22 Apr 2020 11:09:22: 8000000 INFO @ Wed, 22 Apr 2020 11:09:23: 3000000 INFO @ Wed, 22 Apr 2020 11:09:28: 9000000 INFO @ Wed, 22 Apr 2020 11:09:29: 4000000 INFO @ Wed, 22 Apr 2020 11:09:33: 10000000 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 11:09:34: 5000000 INFO @ Wed, 22 Apr 2020 11:09:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.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 11:09:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:09:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:09:39: 11000000 INFO @ Wed, 22 Apr 2020 11:09:40: 6000000 INFO @ Wed, 22 Apr 2020 11:09:42: 1000000 INFO @ Wed, 22 Apr 2020 11:09:45: 12000000 INFO @ Wed, 22 Apr 2020 11:09:46: 7000000 INFO @ Wed, 22 Apr 2020 11:09:48: 2000000 INFO @ Wed, 22 Apr 2020 11:09:51: 13000000 INFO @ Wed, 22 Apr 2020 11:09:52: 8000000 INFO @ Wed, 22 Apr 2020 11:09:54: 3000000 INFO @ Wed, 22 Apr 2020 11:09:57: 14000000 INFO @ Wed, 22 Apr 2020 11:09:58: 9000000 INFO @ Wed, 22 Apr 2020 11:10:00: 4000000 INFO @ Wed, 22 Apr 2020 11:10:02: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:10:02: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:10:02: #1 total tags in treatment: 6495292 INFO @ Wed, 22 Apr 2020 11:10:02: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:10:02: #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 11:10:02: #1 tags after filtering in treatment: 3218683 INFO @ Wed, 22 Apr 2020 11:10:02: #1 Redundant rate of treatment: 0.50 INFO @ Wed, 22 Apr 2020 11:10:02: #1 finished! INFO @ Wed, 22 Apr 2020 11:10:02: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:10:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:10:02: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:10:02: Too few paired peaks (0) 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 11:10:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.05_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/SRX7756603/SRX7756603.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:10:04: 10000000 INFO @ Wed, 22 Apr 2020 11:10:06: 5000000 INFO @ Wed, 22 Apr 2020 11:10:10: 11000000 INFO @ Wed, 22 Apr 2020 11:10:11: 6000000 INFO @ Wed, 22 Apr 2020 11:10:16: 12000000 INFO @ Wed, 22 Apr 2020 11:10:17: 7000000 INFO @ Wed, 22 Apr 2020 11:10:22: 13000000 INFO @ Wed, 22 Apr 2020 11:10:22: 8000000 INFO @ Wed, 22 Apr 2020 11:10:27: 14000000 INFO @ Wed, 22 Apr 2020 11:10:28: 9000000 INFO @ Wed, 22 Apr 2020 11:10:33: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:10:33: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:10:33: #1 total tags in treatment: 6495292 INFO @ Wed, 22 Apr 2020 11:10:33: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:10:33: #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 11:10:33: #1 tags after filtering in treatment: 3218683 INFO @ Wed, 22 Apr 2020 11:10:33: #1 Redundant rate of treatment: 0.50 INFO @ Wed, 22 Apr 2020 11:10:33: #1 finished! INFO @ Wed, 22 Apr 2020 11:10:33: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:10:33: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:10:33: Too few paired peaks (0) 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 11:10:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.10_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/SRX7756603/SRX7756603.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:10:33: 10000000 INFO @ Wed, 22 Apr 2020 11:10:39: 11000000 INFO @ Wed, 22 Apr 2020 11:10:44: 12000000 INFO @ Wed, 22 Apr 2020 11:10:50: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:10:55: 14000000 INFO @ Wed, 22 Apr 2020 11:11:00: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:11:00: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:11:00: #1 total tags in treatment: 6495292 INFO @ Wed, 22 Apr 2020 11:11:00: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:11:00: #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 11:11:00: #1 tags after filtering in treatment: 3218683 INFO @ Wed, 22 Apr 2020 11:11:00: #1 Redundant rate of treatment: 0.50 INFO @ Wed, 22 Apr 2020 11:11:00: #1 finished! INFO @ Wed, 22 Apr 2020 11:11:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:11:00: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:11:00: Too few paired peaks (0) 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 11:11:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.20_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/SRX7756603/SRX7756603.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756603/SRX7756603.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。