Job ID = 7116845 SRX = SRX8639488 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:19:00 prefetch.2.10.7: 1) Downloading 'SRR12117052'... 2020-07-22T06:19:00 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:21:01 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:21:01 prefetch.2.10.7: 1) 'SRR12117052' was downloaded successfully 2020-07-22T06:21:01 prefetch.2.10.7: 'SRR12117052' has 0 unresolved dependencies Read 23786522 spots for SRR12117052/SRR12117052.sra Written 23786522 spots for SRR12117052/SRR12117052.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: 00:07:37 23786522 reads; of these: 23786522 (100.00%) were paired; of these: 10764424 (45.25%) aligned concordantly 0 times 11974220 (50.34%) aligned concordantly exactly 1 time 1047878 (4.41%) aligned concordantly >1 times ---- 10764424 pairs aligned concordantly 0 times; of these: 73201 (0.68%) aligned discordantly 1 time ---- 10691223 pairs aligned 0 times concordantly or discordantly; of these: 21382446 mates make up the pairs; of these: 21176519 (99.04%) aligned 0 times 173842 (0.81%) aligned exactly 1 time 32085 (0.15%) aligned >1 times 55.49% overall alignment rate Time searching: 00:07:37 Overall time: 00:07:37 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] 154038 / 13080490 = 0.0118 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 15:36:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.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 15:36:03: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:36:03: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:36:08: 1000000 INFO @ Wed, 22 Jul 2020 15:36:13: 2000000 INFO @ Wed, 22 Jul 2020 15:36:18: 3000000 INFO @ Wed, 22 Jul 2020 15:36:23: 4000000 INFO @ Wed, 22 Jul 2020 15:36:28: 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 15:36:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.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 15:36:33: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:36:33: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:36:33: 6000000 INFO @ Wed, 22 Jul 2020 15:36:38: 1000000 INFO @ Wed, 22 Jul 2020 15:36:38: 7000000 INFO @ Wed, 22 Jul 2020 15:36:44: 8000000 INFO @ Wed, 22 Jul 2020 15:36:44: 2000000 INFO @ Wed, 22 Jul 2020 15:36:50: 9000000 INFO @ Wed, 22 Jul 2020 15:36:50: 3000000 INFO @ Wed, 22 Jul 2020 15:36:56: 10000000 INFO @ Wed, 22 Jul 2020 15:36:56: 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 15:37:01: 11000000 INFO @ Wed, 22 Jul 2020 15:37:01: 5000000 INFO @ Wed, 22 Jul 2020 15:37:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.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 15:37:03: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:37:03: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:37:07: 6000000 INFO @ Wed, 22 Jul 2020 15:37:07: 12000000 INFO @ Wed, 22 Jul 2020 15:37:09: 1000000 INFO @ Wed, 22 Jul 2020 15:37:13: 7000000 INFO @ Wed, 22 Jul 2020 15:37:13: 13000000 INFO @ Wed, 22 Jul 2020 15:37:15: 2000000 INFO @ Wed, 22 Jul 2020 15:37:19: 8000000 INFO @ Wed, 22 Jul 2020 15:37:19: 14000000 INFO @ Wed, 22 Jul 2020 15:37:20: 3000000 INFO @ Wed, 22 Jul 2020 15:37:25: 9000000 INFO @ Wed, 22 Jul 2020 15:37:25: 15000000 INFO @ Wed, 22 Jul 2020 15:37:26: 4000000 INFO @ Wed, 22 Jul 2020 15:37:30: 10000000 INFO @ Wed, 22 Jul 2020 15:37:31: 16000000 INFO @ Wed, 22 Jul 2020 15:37:32: 5000000 INFO @ Wed, 22 Jul 2020 15:37:36: 11000000 INFO @ Wed, 22 Jul 2020 15:37:36: 17000000 INFO @ Wed, 22 Jul 2020 15:37:38: 6000000 INFO @ Wed, 22 Jul 2020 15:37:42: 12000000 INFO @ Wed, 22 Jul 2020 15:37:42: 18000000 INFO @ Wed, 22 Jul 2020 15:37:44: 7000000 INFO @ Wed, 22 Jul 2020 15:37:48: 13000000 INFO @ Wed, 22 Jul 2020 15:37:48: 19000000 INFO @ Wed, 22 Jul 2020 15:37:50: 8000000 INFO @ Wed, 22 Jul 2020 15:37:54: 14000000 INFO @ Wed, 22 Jul 2020 15:37:54: 20000000 INFO @ Wed, 22 Jul 2020 15:37:55: 9000000 INFO @ Wed, 22 Jul 2020 15:38:00: 15000000 INFO @ Wed, 22 Jul 2020 15:38:00: 21000000 INFO @ Wed, 22 Jul 2020 15:38:01: 10000000 INFO @ Wed, 22 Jul 2020 15:38:05: 16000000 INFO @ Wed, 22 Jul 2020 15:38:05: 22000000 INFO @ Wed, 22 Jul 2020 15:38:07: 11000000 INFO @ Wed, 22 Jul 2020 15:38:11: 17000000 INFO @ Wed, 22 Jul 2020 15:38:11: 23000000 INFO @ Wed, 22 Jul 2020 15:38:13: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 15:38:17: 24000000 INFO @ Wed, 22 Jul 2020 15:38:17: 18000000 INFO @ Wed, 22 Jul 2020 15:38:19: 13000000 INFO @ Wed, 22 Jul 2020 15:38:23: 25000000 INFO @ Wed, 22 Jul 2020 15:38:23: 19000000 INFO @ Wed, 22 Jul 2020 15:38:25: 14000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 15:38:28: 26000000 INFO @ Wed, 22 Jul 2020 15:38:28: 20000000 INFO @ Wed, 22 Jul 2020 15:38:29: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 15:38:29: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 15:38:29: #1 total tags in treatment: 12868118 INFO @ Wed, 22 Jul 2020 15:38:29: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:38:29: #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 15:38:29: #1 tags after filtering in treatment: 8724323 INFO @ Wed, 22 Jul 2020 15:38:29: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 22 Jul 2020 15:38:29: #1 finished! INFO @ Wed, 22 Jul 2020 15:38:29: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:38:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:38:30: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 15:38:30: 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 15:38:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.05_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/SRX8639488/SRX8639488.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:38:30: 15000000 INFO @ Wed, 22 Jul 2020 15:38:34: 21000000 INFO @ Wed, 22 Jul 2020 15:38:36: 16000000 INFO @ Wed, 22 Jul 2020 15:38:40: 22000000 INFO @ Wed, 22 Jul 2020 15:38:42: 17000000 INFO @ Wed, 22 Jul 2020 15:38:45: 23000000 INFO @ Wed, 22 Jul 2020 15:38:47: 18000000 INFO @ Wed, 22 Jul 2020 15:38:51: 24000000 INFO @ Wed, 22 Jul 2020 15:38:53: 19000000 INFO @ Wed, 22 Jul 2020 15:38:56: 25000000 INFO @ Wed, 22 Jul 2020 15:38:59: 20000000 INFO @ Wed, 22 Jul 2020 15:39:02: 26000000 INFO @ Wed, 22 Jul 2020 15:39:02: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 15:39:02: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 15:39:02: #1 total tags in treatment: 12868118 INFO @ Wed, 22 Jul 2020 15:39:02: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:39:02: #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 15:39:03: #1 tags after filtering in treatment: 8724323 INFO @ Wed, 22 Jul 2020 15:39:03: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 22 Jul 2020 15:39:03: #1 finished! INFO @ Wed, 22 Jul 2020 15:39:03: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:39:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:39:03: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 15:39:03: 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 15:39:03: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.10_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/SRX8639488/SRX8639488.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:39:04: 21000000 INFO @ Wed, 22 Jul 2020 15:39:09: 22000000 INFO @ Wed, 22 Jul 2020 15:39:14: 23000000 INFO @ Wed, 22 Jul 2020 15:39:19: 24000000 INFO @ Wed, 22 Jul 2020 15:39:24: 25000000 INFO @ Wed, 22 Jul 2020 15:39:29: 26000000 INFO @ Wed, 22 Jul 2020 15:39:29: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 15:39:29: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 15:39:29: #1 total tags in treatment: 12868118 INFO @ Wed, 22 Jul 2020 15:39:29: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:39:29: #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 15:39:29: #1 tags after filtering in treatment: 8724323 INFO @ Wed, 22 Jul 2020 15:39:29: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 22 Jul 2020 15:39:29: #1 finished! INFO @ Wed, 22 Jul 2020 15:39:29: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:39:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:39:30: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 15:39:30: 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 15:39:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.20_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/SRX8639488/SRX8639488.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639488/SRX8639488.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling