Job ID = 7114459 SRX = SRX8462200 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:58:06 prefetch.2.10.7: 1) Downloading 'SRR11915659'... 2020-07-22T05:58:06 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:59:38 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:59:38 prefetch.2.10.7: 'SRR11915659' is valid 2020-07-22T05:59:38 prefetch.2.10.7: 1) 'SRR11915659' was downloaded successfully 2020-07-22T05:59:38 prefetch.2.10.7: 'SRR11915659' has 0 unresolved dependencies Read 6630611 spots for SRR11915659/SRR11915659.sra Written 6630611 spots for SRR11915659/SRR11915659.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: 00:05:21 6630611 reads; of these: 6630611 (100.00%) were paired; of these: 832226 (12.55%) aligned concordantly 0 times 5004807 (75.48%) aligned concordantly exactly 1 time 793578 (11.97%) aligned concordantly >1 times ---- 832226 pairs aligned concordantly 0 times; of these: 39087 (4.70%) aligned discordantly 1 time ---- 793139 pairs aligned 0 times concordantly or discordantly; of these: 1586278 mates make up the pairs; of these: 1448748 (91.33%) aligned 0 times 104655 (6.60%) aligned exactly 1 time 32875 (2.07%) aligned >1 times 89.08% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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] 1613192 / 5832237 = 0.2766 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 15:09:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.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 15:09:40: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:09:40: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:09:46: 1000000 INFO @ Wed, 22 Jul 2020 15:09:52: 2000000 INFO @ Wed, 22 Jul 2020 15:09:59: 3000000 INFO @ Wed, 22 Jul 2020 15:10:05: 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 15:10:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.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 15:10:10: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:10:10: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:10:11: 5000000 INFO @ Wed, 22 Jul 2020 15:10:17: 1000000 INFO @ Wed, 22 Jul 2020 15:10:17: 6000000 INFO @ Wed, 22 Jul 2020 15:10:24: 2000000 INFO @ Wed, 22 Jul 2020 15:10:24: 7000000 INFO @ Wed, 22 Jul 2020 15:10:31: 3000000 INFO @ Wed, 22 Jul 2020 15:10:31: 8000000 INFO @ Wed, 22 Jul 2020 15:10:35: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:10:35: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:10:35: #1 total tags in treatment: 4188924 INFO @ Wed, 22 Jul 2020 15:10:35: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:10:35: #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 15:10:35: #1 tags after filtering in treatment: 3416370 INFO @ Wed, 22 Jul 2020 15:10:35: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Jul 2020 15:10:35: #1 finished! INFO @ Wed, 22 Jul 2020 15:10:35: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:10:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:10:35: #2 number of paired peaks: 28 WARNING @ Wed, 22 Jul 2020 15:10:35: Too few paired peaks (28) 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 15:10:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.05_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/SRX8462200/SRX8462200.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:10:37: 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 15:10:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.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 15:10:40: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:10:40: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:10:44: 5000000 INFO @ Wed, 22 Jul 2020 15:10:47: 1000000 INFO @ Wed, 22 Jul 2020 15:10:51: 6000000 INFO @ Wed, 22 Jul 2020 15:10:54: 2000000 INFO @ Wed, 22 Jul 2020 15:10:58: 7000000 INFO @ Wed, 22 Jul 2020 15:11:01: 3000000 INFO @ Wed, 22 Jul 2020 15:11:05: 8000000 INFO @ Wed, 22 Jul 2020 15:11:08: 4000000 INFO @ Wed, 22 Jul 2020 15:11:09: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:11:09: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:11:09: #1 total tags in treatment: 4188924 INFO @ Wed, 22 Jul 2020 15:11:09: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:11:09: #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 15:11:09: #1 tags after filtering in treatment: 3416370 INFO @ Wed, 22 Jul 2020 15:11:09: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Jul 2020 15:11:09: #1 finished! INFO @ Wed, 22 Jul 2020 15:11:09: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:11:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:11:09: #2 number of paired peaks: 28 WARNING @ Wed, 22 Jul 2020 15:11:09: Too few paired peaks (28) 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 15:11:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.10_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/SRX8462200/SRX8462200.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:11:15: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 15:11:21: 6000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 15:11:28: 7000000 INFO @ Wed, 22 Jul 2020 15:11:35: 8000000 INFO @ Wed, 22 Jul 2020 15:11:39: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:11:39: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:11:39: #1 total tags in treatment: 4188924 INFO @ Wed, 22 Jul 2020 15:11:39: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:11:39: #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 15:11:39: #1 tags after filtering in treatment: 3416370 INFO @ Wed, 22 Jul 2020 15:11:39: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Jul 2020 15:11:39: #1 finished! INFO @ Wed, 22 Jul 2020 15:11:39: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:11:39: #2 number of paired peaks: 28 WARNING @ Wed, 22 Jul 2020 15:11:39: Too few paired peaks (28) 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 15:11:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.20_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/SRX8462200/SRX8462200.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462200/SRX8462200.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling