Job ID = 7117947 SRX = SRX8639562 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T07:00:15 prefetch.2.10.7: 1) Downloading 'SRR12117000'... 2020-07-22T07:00:15 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T07:07:28 prefetch.2.10.7: HTTPS download succeed 2020-07-22T07:07:28 prefetch.2.10.7: 1) 'SRR12117000' was downloaded successfully 2020-07-22T07:07:28 prefetch.2.10.7: 'SRR12117000' has 0 unresolved dependencies Read 25735914 spots for SRR12117000/SRR12117000.sra Written 25735914 spots for SRR12117000/SRR12117000.sra 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: 00:02:45 25735914 reads; of these: 25735914 (100.00%) were paired; of these: 24256193 (94.25%) aligned concordantly 0 times 1309492 (5.09%) aligned concordantly exactly 1 time 170229 (0.66%) aligned concordantly >1 times ---- 24256193 pairs aligned concordantly 0 times; of these: 3860 (0.02%) aligned discordantly 1 time ---- 24252333 pairs aligned 0 times concordantly or discordantly; of these: 48504666 mates make up the pairs; of these: 48446826 (99.88%) aligned 0 times 38444 (0.08%) aligned exactly 1 time 19396 (0.04%) aligned >1 times 5.88% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 12037 / 1482929 = 0.0081 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 Jul 2020 16:13:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.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 Jul 2020 16:13:26: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:13:26: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:13:30: 1000000 INFO @ Wed, 22 Jul 2020 16:13:35: 2000000 INFO @ Wed, 22 Jul 2020 16:13:39: 3000000 INFO @ Wed, 22 Jul 2020 16:13:39: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:13:39: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:13:39: #1 total tags in treatment: 1467684 INFO @ Wed, 22 Jul 2020 16:13:39: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:13:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:13:39: #1 tags after filtering in treatment: 1376842 INFO @ Wed, 22 Jul 2020 16:13:39: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 22 Jul 2020 16:13:39: #1 finished! INFO @ Wed, 22 Jul 2020 16:13:39: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:13:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:13:39: #2 number of paired peaks: 37 WARNING @ Wed, 22 Jul 2020 16:13:39: Too few paired peaks (37) 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 Jul 2020 16:13:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.05_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/SRX8639562/SRX8639562.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 Jul 2020 16:13:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.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 Jul 2020 16:13:56: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:13:56: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:14:00: 1000000 INFO @ Wed, 22 Jul 2020 16:14:05: 2000000 INFO @ Wed, 22 Jul 2020 16:14:09: 3000000 INFO @ Wed, 22 Jul 2020 16:14:09: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:14:09: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:14:09: #1 total tags in treatment: 1467684 INFO @ Wed, 22 Jul 2020 16:14:09: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:14:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:14:09: #1 tags after filtering in treatment: 1376842 INFO @ Wed, 22 Jul 2020 16:14:09: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 22 Jul 2020 16:14:09: #1 finished! INFO @ Wed, 22 Jul 2020 16:14:09: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:14:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:14:09: #2 number of paired peaks: 37 WARNING @ Wed, 22 Jul 2020 16:14:09: Too few paired peaks (37) 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 Jul 2020 16:14:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.10_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/SRX8639562/SRX8639562.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 Jul 2020 16:14:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.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 Jul 2020 16:14:26: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:14:26: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:14:31: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:14:37: 2000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:14:42: 3000000 INFO @ Wed, 22 Jul 2020 16:14:42: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:14:42: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:14:42: #1 total tags in treatment: 1467684 INFO @ Wed, 22 Jul 2020 16:14:42: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:14:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:14:42: #1 tags after filtering in treatment: 1376842 INFO @ Wed, 22 Jul 2020 16:14:42: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 22 Jul 2020 16:14:42: #1 finished! INFO @ Wed, 22 Jul 2020 16:14:42: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:14:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:14:42: #2 number of paired peaks: 37 WARNING @ Wed, 22 Jul 2020 16:14:42: Too few paired peaks (37) 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 Jul 2020 16:14:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.20_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/SRX8639562/SRX8639562.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639562/SRX8639562.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling