Job ID = 7114470 SRX = SRX8462201 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:58:33 prefetch.2.10.7: 1) Downloading 'SRR11915660'... 2020-07-22T05:58:33 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:00:23 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:00:24 prefetch.2.10.7: 'SRR11915660' is valid 2020-07-22T06:00:24 prefetch.2.10.7: 1) 'SRR11915660' was downloaded successfully 2020-07-22T06:00:24 prefetch.2.10.7: 'SRR11915660' has 0 unresolved dependencies Read 7054432 spots for SRR11915660/SRR11915660.sra Written 7054432 spots for SRR11915660/SRR11915660.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: 00:05:28 7054432 reads; of these: 7054432 (100.00%) were paired; of these: 931169 (13.20%) aligned concordantly 0 times 5212509 (73.89%) aligned concordantly exactly 1 time 910754 (12.91%) aligned concordantly >1 times ---- 931169 pairs aligned concordantly 0 times; of these: 43545 (4.68%) aligned discordantly 1 time ---- 887624 pairs aligned 0 times concordantly or discordantly; of these: 1775248 mates make up the pairs; of these: 1627850 (91.70%) aligned 0 times 108567 (6.12%) aligned exactly 1 time 38831 (2.19%) aligned >1 times 88.46% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 3456358 / 6162361 = 0.5609 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 15:10:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.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 15:10:15: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:10:15: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:10:21: 1000000 INFO @ Wed, 22 Jul 2020 15:10:27: 2000000 INFO @ Wed, 22 Jul 2020 15:10:33: 3000000 INFO @ Wed, 22 Jul 2020 15:10:39: 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 15:10:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.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 15:10:45: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:10:45: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:10:45: 5000000 INFO @ Wed, 22 Jul 2020 15:10:49: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:10:49: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:10:49: #1 total tags in treatment: 2676190 INFO @ Wed, 22 Jul 2020 15:10:49: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:10:49: #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 15:10:49: #1 tags after filtering in treatment: 2117351 INFO @ Wed, 22 Jul 2020 15:10:49: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Jul 2020 15:10:49: #1 finished! INFO @ Wed, 22 Jul 2020 15:10:49: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:10:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:10:49: #2 number of paired peaks: 41 WARNING @ Wed, 22 Jul 2020 15:10:49: Too few paired peaks (41) 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 15:10:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.05_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/SRX8462201/SRX8462201.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:10:52: 1000000 INFO @ Wed, 22 Jul 2020 15:10:58: 2000000 INFO @ Wed, 22 Jul 2020 15:11:04: 3000000 INFO @ Wed, 22 Jul 2020 15:11:10: 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 15:11:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.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 15:11:15: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:11:15: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:11:17: 5000000 INFO @ Wed, 22 Jul 2020 15:11:21: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:11:21: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:11:21: #1 total tags in treatment: 2676190 INFO @ Wed, 22 Jul 2020 15:11:21: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:11:21: #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 15:11:21: #1 tags after filtering in treatment: 2117351 INFO @ Wed, 22 Jul 2020 15:11:21: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Jul 2020 15:11:21: #1 finished! INFO @ Wed, 22 Jul 2020 15:11:21: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:11:21: #2 number of paired peaks: 41 WARNING @ Wed, 22 Jul 2020 15:11:21: Too few paired peaks (41) 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 15:11:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.10_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/SRX8462201/SRX8462201.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:11:22: 1000000 INFO @ Wed, 22 Jul 2020 15:11:29: 2000000 INFO @ Wed, 22 Jul 2020 15:11:35: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 15:11:42: 4000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 15:11:49: 5000000 INFO @ Wed, 22 Jul 2020 15:11:52: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:11:52: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:11:52: #1 total tags in treatment: 2676190 INFO @ Wed, 22 Jul 2020 15:11:52: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:11:52: #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 15:11:52: #1 tags after filtering in treatment: 2117351 INFO @ Wed, 22 Jul 2020 15:11:52: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Jul 2020 15:11:52: #1 finished! INFO @ Wed, 22 Jul 2020 15:11:52: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:11:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:11:52: #2 number of paired peaks: 41 WARNING @ Wed, 22 Jul 2020 15:11:52: Too few paired peaks (41) 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 15:11:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.20_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/SRX8462201/SRX8462201.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462201/SRX8462201.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling