Job ID = 7117808 SRX = SRX8639555 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:45:41 prefetch.2.10.7: 1) Downloading 'SRR12116993'... 2020-07-22T06:45:41 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:47:19 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:47:19 prefetch.2.10.7: 1) 'SRR12116993' was downloaded successfully 2020-07-22T06:47:19 prefetch.2.10.7: 'SRR12116993' has 0 unresolved dependencies Read 21436138 spots for SRR12116993/SRR12116993.sra Written 21436138 spots for SRR12116993/SRR12116993.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: 00:09:00 21436138 reads; of these: 21436138 (100.00%) were paired; of these: 4970886 (23.19%) aligned concordantly 0 times 14442277 (67.37%) aligned concordantly exactly 1 time 2022975 (9.44%) aligned concordantly >1 times ---- 4970886 pairs aligned concordantly 0 times; of these: 117179 (2.36%) aligned discordantly 1 time ---- 4853707 pairs aligned 0 times concordantly or discordantly; of these: 9707414 mates make up the pairs; of these: 9462506 (97.48%) aligned 0 times 173745 (1.79%) aligned exactly 1 time 71163 (0.73%) aligned >1 times 77.93% overall alignment rate Time searching: 00:09:00 Overall time: 00:09:00 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 16 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] 294616 / 16561789 = 0.0178 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 16:04:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.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 16:04:50: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:04:50: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:04:56: 1000000 INFO @ Wed, 22 Jul 2020 16:05:01: 2000000 INFO @ Wed, 22 Jul 2020 16:05:06: 3000000 INFO @ Wed, 22 Jul 2020 16:05:12: 4000000 INFO @ Wed, 22 Jul 2020 16:05:17: 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 16:05:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.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 16:05:20: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:05:20: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:05:23: 6000000 INFO @ Wed, 22 Jul 2020 16:05:27: 1000000 INFO @ Wed, 22 Jul 2020 16:05:29: 7000000 INFO @ Wed, 22 Jul 2020 16:05:35: 2000000 INFO @ Wed, 22 Jul 2020 16:05:36: 8000000 INFO @ Wed, 22 Jul 2020 16:05:42: 3000000 INFO @ Wed, 22 Jul 2020 16:05:42: 9000000 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 16:05:49: 10000000 INFO @ Wed, 22 Jul 2020 16:05:49: 4000000 INFO @ Wed, 22 Jul 2020 16:05:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.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 16:05:50: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:05:50: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:05:56: 11000000 INFO @ Wed, 22 Jul 2020 16:05:57: 5000000 INFO @ Wed, 22 Jul 2020 16:05:58: 1000000 INFO @ Wed, 22 Jul 2020 16:06:03: 12000000 INFO @ Wed, 22 Jul 2020 16:06:05: 2000000 INFO @ Wed, 22 Jul 2020 16:06:05: 6000000 INFO @ Wed, 22 Jul 2020 16:06:10: 13000000 INFO @ Wed, 22 Jul 2020 16:06:11: 3000000 INFO @ Wed, 22 Jul 2020 16:06:13: 7000000 INFO @ Wed, 22 Jul 2020 16:06:17: 14000000 INFO @ Wed, 22 Jul 2020 16:06:18: 4000000 INFO @ Wed, 22 Jul 2020 16:06:21: 8000000 INFO @ Wed, 22 Jul 2020 16:06:24: 15000000 INFO @ Wed, 22 Jul 2020 16:06:25: 5000000 INFO @ Wed, 22 Jul 2020 16:06:28: 9000000 INFO @ Wed, 22 Jul 2020 16:06:31: 16000000 INFO @ Wed, 22 Jul 2020 16:06:32: 6000000 INFO @ Wed, 22 Jul 2020 16:06:36: 10000000 INFO @ Wed, 22 Jul 2020 16:06:38: 17000000 INFO @ Wed, 22 Jul 2020 16:06:39: 7000000 INFO @ Wed, 22 Jul 2020 16:06:44: 11000000 INFO @ Wed, 22 Jul 2020 16:06:45: 18000000 INFO @ Wed, 22 Jul 2020 16:06:46: 8000000 INFO @ Wed, 22 Jul 2020 16:06:51: 12000000 INFO @ Wed, 22 Jul 2020 16:06:52: 19000000 INFO @ Wed, 22 Jul 2020 16:06:53: 9000000 INFO @ Wed, 22 Jul 2020 16:06:59: 20000000 INFO @ Wed, 22 Jul 2020 16:06:59: 13000000 INFO @ Wed, 22 Jul 2020 16:07:00: 10000000 INFO @ Wed, 22 Jul 2020 16:07:06: 21000000 INFO @ Wed, 22 Jul 2020 16:07:06: 14000000 INFO @ Wed, 22 Jul 2020 16:07:07: 11000000 INFO @ Wed, 22 Jul 2020 16:07:13: 22000000 INFO @ Wed, 22 Jul 2020 16:07:13: 12000000 INFO @ Wed, 22 Jul 2020 16:07:14: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:07:20: 23000000 INFO @ Wed, 22 Jul 2020 16:07:20: 13000000 INFO @ Wed, 22 Jul 2020 16:07:21: 16000000 INFO @ Wed, 22 Jul 2020 16:07:27: 24000000 INFO @ Wed, 22 Jul 2020 16:07:27: 14000000 INFO @ Wed, 22 Jul 2020 16:07:28: 17000000 INFO @ Wed, 22 Jul 2020 16:07:34: 25000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:07:34: 15000000 INFO @ Wed, 22 Jul 2020 16:07:35: 18000000 INFO @ Wed, 22 Jul 2020 16:07:41: 26000000 INFO @ Wed, 22 Jul 2020 16:07:41: 16000000 INFO @ Wed, 22 Jul 2020 16:07:43: 19000000 INFO @ Wed, 22 Jul 2020 16:07:48: 27000000 INFO @ Wed, 22 Jul 2020 16:07:48: 17000000 INFO @ Wed, 22 Jul 2020 16:07:51: 20000000 INFO @ Wed, 22 Jul 2020 16:07:55: 28000000 INFO @ Wed, 22 Jul 2020 16:07:55: 18000000 INFO @ Wed, 22 Jul 2020 16:07:58: 21000000 INFO @ Wed, 22 Jul 2020 16:08:02: 29000000 INFO @ Wed, 22 Jul 2020 16:08:02: 19000000 INFO @ Wed, 22 Jul 2020 16:08:06: 22000000 INFO @ Wed, 22 Jul 2020 16:08:09: 30000000 INFO @ Wed, 22 Jul 2020 16:08:09: 20000000 INFO @ Wed, 22 Jul 2020 16:08:13: 23000000 INFO @ Wed, 22 Jul 2020 16:08:15: 31000000 INFO @ Wed, 22 Jul 2020 16:08:16: 21000000 INFO @ Wed, 22 Jul 2020 16:08:21: 24000000 INFO @ Wed, 22 Jul 2020 16:08:22: 32000000 INFO @ Wed, 22 Jul 2020 16:08:24: 22000000 INFO @ Wed, 22 Jul 2020 16:08:28: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:08:28: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:08:28: #1 total tags in treatment: 16170841 INFO @ Wed, 22 Jul 2020 16:08:28: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:08:28: #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 16:08:28: #1 tags after filtering in treatment: 11006945 INFO @ Wed, 22 Jul 2020 16:08:28: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 22 Jul 2020 16:08:28: #1 finished! INFO @ Wed, 22 Jul 2020 16:08:28: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:08:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:08:28: 25000000 INFO @ Wed, 22 Jul 2020 16:08:29: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:08:29: 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 16:08:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.05_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/SRX8639555/SRX8639555.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:08:30: 23000000 INFO @ Wed, 22 Jul 2020 16:08:37: 26000000 INFO @ Wed, 22 Jul 2020 16:08:37: 24000000 INFO @ Wed, 22 Jul 2020 16:08:44: 25000000 INFO @ Wed, 22 Jul 2020 16:08:45: 27000000 INFO @ Wed, 22 Jul 2020 16:08:51: 26000000 INFO @ Wed, 22 Jul 2020 16:08:52: 28000000 INFO @ Wed, 22 Jul 2020 16:08:58: 27000000 INFO @ Wed, 22 Jul 2020 16:08:59: 29000000 INFO @ Wed, 22 Jul 2020 16:09:04: 28000000 INFO @ Wed, 22 Jul 2020 16:09:07: 30000000 INFO @ Wed, 22 Jul 2020 16:09:11: 29000000 INFO @ Wed, 22 Jul 2020 16:09:14: 31000000 INFO @ Wed, 22 Jul 2020 16:09:18: 30000000 INFO @ Wed, 22 Jul 2020 16:09:21: 32000000 INFO @ Wed, 22 Jul 2020 16:09:25: 31000000 INFO @ Wed, 22 Jul 2020 16:09:27: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:09:27: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:09:27: #1 total tags in treatment: 16170841 INFO @ Wed, 22 Jul 2020 16:09:27: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:09:27: #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 16:09:27: #1 tags after filtering in treatment: 11006945 INFO @ Wed, 22 Jul 2020 16:09:27: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 22 Jul 2020 16:09:27: #1 finished! INFO @ Wed, 22 Jul 2020 16:09:27: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:09:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:09:28: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:09:28: 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 16:09:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.10_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/SRX8639555/SRX8639555.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:09:31: 32000000 INFO @ Wed, 22 Jul 2020 16:09:36: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:09:36: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:09:36: #1 total tags in treatment: 16170841 INFO @ Wed, 22 Jul 2020 16:09:36: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:09:36: #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 16:09:36: #1 tags after filtering in treatment: 11006945 INFO @ Wed, 22 Jul 2020 16:09:36: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 22 Jul 2020 16:09:36: #1 finished! INFO @ Wed, 22 Jul 2020 16:09:36: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:09:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:09:37: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:09:37: 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 16:09:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.20_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/SRX8639555/SRX8639555.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639555/SRX8639555.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling