Job ID = 7113898 SRX = SRX8462184 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:47:22 prefetch.2.10.7: 1) Downloading 'SRR11915643'... 2020-07-22T05:47:22 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:48:40 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:48:40 prefetch.2.10.7: 'SRR11915643' is valid 2020-07-22T05:48:40 prefetch.2.10.7: 1) 'SRR11915643' was downloaded successfully 2020-07-22T05:48:40 prefetch.2.10.7: 'SRR11915643' has 0 unresolved dependencies Read 6675044 spots for SRR11915643/SRR11915643.sra Written 6675044 spots for SRR11915643/SRR11915643.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: 00:06:16 6675044 reads; of these: 6675044 (100.00%) were paired; of these: 826254 (12.38%) aligned concordantly 0 times 4846931 (72.61%) aligned concordantly exactly 1 time 1001859 (15.01%) aligned concordantly >1 times ---- 826254 pairs aligned concordantly 0 times; of these: 54649 (6.61%) aligned discordantly 1 time ---- 771605 pairs aligned 0 times concordantly or discordantly; of these: 1543210 mates make up the pairs; of these: 1392766 (90.25%) aligned 0 times 105916 (6.86%) aligned exactly 1 time 44528 (2.89%) aligned >1 times 89.57% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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] 2104364 / 5900039 = 0.3567 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 14:59:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.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 14:59:54: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:59:54: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:00:00: 1000000 INFO @ Wed, 22 Jul 2020 15:00:05: 2000000 INFO @ Wed, 22 Jul 2020 15:00:11: 3000000 INFO @ Wed, 22 Jul 2020 15:00:17: 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 Jul 2020 15:00:22: 5000000 INFO @ Wed, 22 Jul 2020 15:00:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.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 15:00:23: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:00:23: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:00:29: 6000000 INFO @ Wed, 22 Jul 2020 15:00:29: 1000000 INFO @ Wed, 22 Jul 2020 15:00:35: 7000000 INFO @ Wed, 22 Jul 2020 15:00:35: 2000000 INFO @ Wed, 22 Jul 2020 15:00:39: #1 tag size is determined as 76 bps INFO @ Wed, 22 Jul 2020 15:00:39: #1 tag size = 76 INFO @ Wed, 22 Jul 2020 15:00:39: #1 total tags in treatment: 3750914 INFO @ Wed, 22 Jul 2020 15:00:39: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:00:39: #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 15:00:39: #1 tags after filtering in treatment: 2880392 INFO @ Wed, 22 Jul 2020 15:00:39: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Jul 2020 15:00:39: #1 finished! INFO @ Wed, 22 Jul 2020 15:00:39: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:00:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:00:39: #2 number of paired peaks: 30 WARNING @ Wed, 22 Jul 2020 15:00:39: 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 Jul 2020 15:00:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.05_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/SRX8462184/SRX8462184.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:00:41: 3000000 INFO @ Wed, 22 Jul 2020 15:00:47: 4000000 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 15:00:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.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 15:00:53: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:00:53: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:00:53: 5000000 INFO @ Wed, 22 Jul 2020 15:00:59: 6000000 INFO @ Wed, 22 Jul 2020 15:01:00: 1000000 INFO @ Wed, 22 Jul 2020 15:01:06: 7000000 INFO @ Wed, 22 Jul 2020 15:01:07: 2000000 INFO @ Wed, 22 Jul 2020 15:01:10: #1 tag size is determined as 76 bps INFO @ Wed, 22 Jul 2020 15:01:10: #1 tag size = 76 INFO @ Wed, 22 Jul 2020 15:01:10: #1 total tags in treatment: 3750914 INFO @ Wed, 22 Jul 2020 15:01:10: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:01:10: #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 15:01:10: #1 tags after filtering in treatment: 2880392 INFO @ Wed, 22 Jul 2020 15:01:10: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Jul 2020 15:01:10: #1 finished! INFO @ Wed, 22 Jul 2020 15:01:10: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:01:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:01:11: #2 number of paired peaks: 30 WARNING @ Wed, 22 Jul 2020 15:01:11: 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 Jul 2020 15:01:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.10_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/SRX8462184/SRX8462184.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:01:14: 3000000 INFO @ Wed, 22 Jul 2020 15:01:20: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 15:01:27: 5000000 INFO @ Wed, 22 Jul 2020 15:01:34: 6000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 15:01:41: 7000000 INFO @ Wed, 22 Jul 2020 15:01:46: #1 tag size is determined as 76 bps INFO @ Wed, 22 Jul 2020 15:01:46: #1 tag size = 76 INFO @ Wed, 22 Jul 2020 15:01:46: #1 total tags in treatment: 3750914 INFO @ Wed, 22 Jul 2020 15:01:46: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:01:46: #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 15:01:46: #1 tags after filtering in treatment: 2880392 INFO @ Wed, 22 Jul 2020 15:01:46: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Jul 2020 15:01:46: #1 finished! INFO @ Wed, 22 Jul 2020 15:01:46: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:01:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:01:46: #2 number of paired peaks: 30 WARNING @ Wed, 22 Jul 2020 15:01:46: 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 Jul 2020 15:01:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.20_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/SRX8462184/SRX8462184.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462184/SRX8462184.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling