Job ID = 7118177 SRX = SRX8639579 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T07:11:29 prefetch.2.10.7: 1) Downloading 'SRR12117017'... 2020-07-22T07:11:29 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T07:16:57 prefetch.2.10.7: HTTPS download succeed 2020-07-22T07:16:57 prefetch.2.10.7: 1) 'SRR12117017' was downloaded successfully 2020-07-22T07:16:57 prefetch.2.10.7: 'SRR12117017' has 0 unresolved dependencies Read 33099897 spots for SRR12117017/SRR12117017.sra Written 33099897 spots for SRR12117017/SRR12117017.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: 00:09:30 33099897 reads; of these: 33099897 (100.00%) were paired; of these: 20893747 (63.12%) aligned concordantly 0 times 10874533 (32.85%) aligned concordantly exactly 1 time 1331617 (4.02%) aligned concordantly >1 times ---- 20893747 pairs aligned concordantly 0 times; of these: 158365 (0.76%) aligned discordantly 1 time ---- 20735382 pairs aligned 0 times concordantly or discordantly; of these: 41470764 mates make up the pairs; of these: 41187394 (99.32%) aligned 0 times 212992 (0.51%) aligned exactly 1 time 70378 (0.17%) aligned >1 times 37.78% overall alignment rate Time searching: 00:09:30 Overall time: 00:09:30 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] 160975 / 12354533 = 0.0130 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 16:34:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.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 16:34:33: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:34:33: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:34:39: 1000000 INFO @ Wed, 22 Jul 2020 16:34:44: 2000000 INFO @ Wed, 22 Jul 2020 16:34:49: 3000000 INFO @ Wed, 22 Jul 2020 16:34:55: 4000000 INFO @ Wed, 22 Jul 2020 16:35:00: 5000000 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 16:35:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.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 16:35:03: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:35:03: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:35:06: 6000000 INFO @ Wed, 22 Jul 2020 16:35:09: 1000000 INFO @ Wed, 22 Jul 2020 16:35:12: 7000000 INFO @ Wed, 22 Jul 2020 16:35:15: 2000000 INFO @ Wed, 22 Jul 2020 16:35:18: 8000000 INFO @ Wed, 22 Jul 2020 16:35:21: 3000000 INFO @ Wed, 22 Jul 2020 16:35:24: 9000000 INFO @ Wed, 22 Jul 2020 16:35:28: 4000000 INFO @ Wed, 22 Jul 2020 16:35:30: 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 Jul 2020 16:35:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.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 16:35:33: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:35:33: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:35:34: 5000000 INFO @ Wed, 22 Jul 2020 16:35:37: 11000000 INFO @ Wed, 22 Jul 2020 16:35:40: 1000000 INFO @ Wed, 22 Jul 2020 16:35:40: 6000000 INFO @ Wed, 22 Jul 2020 16:35:43: 12000000 INFO @ Wed, 22 Jul 2020 16:35:46: 2000000 INFO @ Wed, 22 Jul 2020 16:35:47: 7000000 INFO @ Wed, 22 Jul 2020 16:35:50: 13000000 INFO @ Wed, 22 Jul 2020 16:35:53: 3000000 INFO @ Wed, 22 Jul 2020 16:35:54: 8000000 INFO @ Wed, 22 Jul 2020 16:35:56: 14000000 INFO @ Wed, 22 Jul 2020 16:35:59: 4000000 INFO @ Wed, 22 Jul 2020 16:36:00: 9000000 INFO @ Wed, 22 Jul 2020 16:36:03: 15000000 INFO @ Wed, 22 Jul 2020 16:36:06: 5000000 INFO @ Wed, 22 Jul 2020 16:36:06: 10000000 INFO @ Wed, 22 Jul 2020 16:36:09: 16000000 INFO @ Wed, 22 Jul 2020 16:36:12: 6000000 INFO @ Wed, 22 Jul 2020 16:36:13: 11000000 INFO @ Wed, 22 Jul 2020 16:36:16: 17000000 INFO @ Wed, 22 Jul 2020 16:36:19: 7000000 INFO @ Wed, 22 Jul 2020 16:36:19: 12000000 INFO @ Wed, 22 Jul 2020 16:36:22: 18000000 INFO @ Wed, 22 Jul 2020 16:36:25: 8000000 INFO @ Wed, 22 Jul 2020 16:36:26: 13000000 INFO @ Wed, 22 Jul 2020 16:36:29: 19000000 INFO @ Wed, 22 Jul 2020 16:36:32: 9000000 INFO @ Wed, 22 Jul 2020 16:36:32: 14000000 INFO @ Wed, 22 Jul 2020 16:36:35: 20000000 INFO @ Wed, 22 Jul 2020 16:36:39: 10000000 INFO @ Wed, 22 Jul 2020 16:36:39: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:36:42: 21000000 INFO @ Wed, 22 Jul 2020 16:36:45: 11000000 INFO @ Wed, 22 Jul 2020 16:36:45: 16000000 INFO @ Wed, 22 Jul 2020 16:36:48: 22000000 INFO @ Wed, 22 Jul 2020 16:36:52: 12000000 INFO @ Wed, 22 Jul 2020 16:36:52: 17000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:36:55: 23000000 INFO @ Wed, 22 Jul 2020 16:36:58: 13000000 INFO @ Wed, 22 Jul 2020 16:36:58: 18000000 INFO @ Wed, 22 Jul 2020 16:37:01: 24000000 INFO @ Wed, 22 Jul 2020 16:37:05: 14000000 INFO @ Wed, 22 Jul 2020 16:37:05: 19000000 INFO @ Wed, 22 Jul 2020 16:37:06: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:37:06: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:37:06: #1 total tags in treatment: 12045365 INFO @ Wed, 22 Jul 2020 16:37:06: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:37:06: #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 16:37:06: #1 tags after filtering in treatment: 7686212 INFO @ Wed, 22 Jul 2020 16:37:06: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 16:37:06: #1 finished! INFO @ Wed, 22 Jul 2020 16:37:06: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:37:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:37:06: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:37:06: 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 Jul 2020 16:37:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.05_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/SRX8639579/SRX8639579.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:37:11: 15000000 INFO @ Wed, 22 Jul 2020 16:37:11: 20000000 INFO @ Wed, 22 Jul 2020 16:37:17: 16000000 INFO @ Wed, 22 Jul 2020 16:37:18: 21000000 INFO @ Wed, 22 Jul 2020 16:37:24: 17000000 INFO @ Wed, 22 Jul 2020 16:37:24: 22000000 INFO @ Wed, 22 Jul 2020 16:37:30: 18000000 INFO @ Wed, 22 Jul 2020 16:37:30: 23000000 INFO @ Wed, 22 Jul 2020 16:37:36: 24000000 INFO @ Wed, 22 Jul 2020 16:37:36: 19000000 INFO @ Wed, 22 Jul 2020 16:37:40: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:37:40: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:37:40: #1 total tags in treatment: 12045365 INFO @ Wed, 22 Jul 2020 16:37:40: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:37:40: #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 16:37:40: #1 tags after filtering in treatment: 7686212 INFO @ Wed, 22 Jul 2020 16:37:40: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 16:37:40: #1 finished! INFO @ Wed, 22 Jul 2020 16:37:40: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:37:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:37:41: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:37:41: 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 Jul 2020 16:37:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.10_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/SRX8639579/SRX8639579.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:37:42: 20000000 INFO @ Wed, 22 Jul 2020 16:37:48: 21000000 INFO @ Wed, 22 Jul 2020 16:37:53: 22000000 INFO @ Wed, 22 Jul 2020 16:37:59: 23000000 INFO @ Wed, 22 Jul 2020 16:38:05: 24000000 INFO @ Wed, 22 Jul 2020 16:38:09: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:38:09: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:38:09: #1 total tags in treatment: 12045365 INFO @ Wed, 22 Jul 2020 16:38:09: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:38:09: #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 16:38:09: #1 tags after filtering in treatment: 7686212 INFO @ Wed, 22 Jul 2020 16:38:09: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 16:38:09: #1 finished! INFO @ Wed, 22 Jul 2020 16:38:09: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:38:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:38:09: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:38:09: 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 Jul 2020 16:38:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.20_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/SRX8639579/SRX8639579.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639579/SRX8639579.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling