Job ID = 7117550 SRX = SRX8639540 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:40:06 prefetch.2.10.7: 1) Downloading 'SRR12116978'... 2020-07-22T06:40:06 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:44:30 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:44:30 prefetch.2.10.7: 1) 'SRR12116978' was downloaded successfully 2020-07-22T06:44:30 prefetch.2.10.7: 'SRR12116978' has 0 unresolved dependencies Read 25417418 spots for SRR12116978/SRR12116978.sra Written 25417418 spots for SRR12116978/SRR12116978.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: 00:11:40 25417418 reads; of these: 25417418 (100.00%) were paired; of these: 5761105 (22.67%) aligned concordantly 0 times 17308925 (68.10%) aligned concordantly exactly 1 time 2347388 (9.24%) aligned concordantly >1 times ---- 5761105 pairs aligned concordantly 0 times; of these: 109381 (1.90%) aligned discordantly 1 time ---- 5651724 pairs aligned 0 times concordantly or discordantly; of these: 11303448 mates make up the pairs; of these: 11039100 (97.66%) aligned 0 times 196658 (1.74%) aligned exactly 1 time 67690 (0.60%) aligned >1 times 78.28% overall alignment rate Time searching: 00:11:40 Overall time: 00:11:40 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 20 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] 384196 / 19731251 = 0.0195 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 16:06:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.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 16:06:36: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:06:36: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:06:41: 1000000 INFO @ Wed, 22 Jul 2020 16:06:45: 2000000 INFO @ Wed, 22 Jul 2020 16:06:50: 3000000 INFO @ Wed, 22 Jul 2020 16:06:55: 4000000 INFO @ Wed, 22 Jul 2020 16:06:59: 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 16:07:04: 6000000 INFO @ Wed, 22 Jul 2020 16:07:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.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 16:07:06: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:07:06: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:07:10: 7000000 INFO @ Wed, 22 Jul 2020 16:07:12: 1000000 INFO @ Wed, 22 Jul 2020 16:07:15: 8000000 INFO @ Wed, 22 Jul 2020 16:07:18: 2000000 INFO @ Wed, 22 Jul 2020 16:07:21: 9000000 INFO @ Wed, 22 Jul 2020 16:07:24: 3000000 INFO @ Wed, 22 Jul 2020 16:07:27: 10000000 INFO @ Wed, 22 Jul 2020 16:07:31: 4000000 INFO @ Wed, 22 Jul 2020 16:07:32: 11000000 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 16:07:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.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 16:07:36: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:07:36: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:07:37: 5000000 INFO @ Wed, 22 Jul 2020 16:07:38: 12000000 INFO @ Wed, 22 Jul 2020 16:07:41: 1000000 INFO @ Wed, 22 Jul 2020 16:07:43: 6000000 INFO @ Wed, 22 Jul 2020 16:07:44: 13000000 INFO @ Wed, 22 Jul 2020 16:07:47: 2000000 INFO @ Wed, 22 Jul 2020 16:07:49: 14000000 INFO @ Wed, 22 Jul 2020 16:07:49: 7000000 INFO @ Wed, 22 Jul 2020 16:07:52: 3000000 INFO @ Wed, 22 Jul 2020 16:07:55: 15000000 INFO @ Wed, 22 Jul 2020 16:07:56: 8000000 INFO @ Wed, 22 Jul 2020 16:07:58: 4000000 INFO @ Wed, 22 Jul 2020 16:08:01: 16000000 INFO @ Wed, 22 Jul 2020 16:08:02: 9000000 INFO @ Wed, 22 Jul 2020 16:08:03: 5000000 INFO @ Wed, 22 Jul 2020 16:08:06: 17000000 INFO @ Wed, 22 Jul 2020 16:08:08: 10000000 INFO @ Wed, 22 Jul 2020 16:08:09: 6000000 INFO @ Wed, 22 Jul 2020 16:08:12: 18000000 INFO @ Wed, 22 Jul 2020 16:08:14: 7000000 INFO @ Wed, 22 Jul 2020 16:08:15: 11000000 INFO @ Wed, 22 Jul 2020 16:08:18: 19000000 INFO @ Wed, 22 Jul 2020 16:08:20: 8000000 INFO @ Wed, 22 Jul 2020 16:08:21: 12000000 INFO @ Wed, 22 Jul 2020 16:08:24: 20000000 INFO @ Wed, 22 Jul 2020 16:08:26: 9000000 INFO @ Wed, 22 Jul 2020 16:08:28: 13000000 INFO @ Wed, 22 Jul 2020 16:08:29: 21000000 INFO @ Wed, 22 Jul 2020 16:08:31: 10000000 INFO @ Wed, 22 Jul 2020 16:08:35: 14000000 INFO @ Wed, 22 Jul 2020 16:08:35: 22000000 INFO @ Wed, 22 Jul 2020 16:08:37: 11000000 INFO @ Wed, 22 Jul 2020 16:08:41: 23000000 INFO @ Wed, 22 Jul 2020 16:08:41: 15000000 INFO @ Wed, 22 Jul 2020 16:08:42: 12000000 INFO @ Wed, 22 Jul 2020 16:08:47: 24000000 INFO @ Wed, 22 Jul 2020 16:08:48: 16000000 INFO @ Wed, 22 Jul 2020 16:08:48: 13000000 INFO @ Wed, 22 Jul 2020 16:08:53: 25000000 INFO @ Wed, 22 Jul 2020 16:08:53: 14000000 INFO @ Wed, 22 Jul 2020 16:08:54: 17000000 INFO @ Wed, 22 Jul 2020 16:08:59: 26000000 INFO @ Wed, 22 Jul 2020 16:08:59: 15000000 INFO @ Wed, 22 Jul 2020 16:09:01: 18000000 INFO @ Wed, 22 Jul 2020 16:09:04: 27000000 INFO @ Wed, 22 Jul 2020 16:09:05: 16000000 INFO @ Wed, 22 Jul 2020 16:09:08: 19000000 INFO @ Wed, 22 Jul 2020 16:09:10: 28000000 INFO @ Wed, 22 Jul 2020 16:09:10: 17000000 INFO @ Wed, 22 Jul 2020 16:09:14: 20000000 INFO @ Wed, 22 Jul 2020 16:09:16: 29000000 INFO @ Wed, 22 Jul 2020 16:09:16: 18000000 INFO @ Wed, 22 Jul 2020 16:09:21: 21000000 INFO @ Wed, 22 Jul 2020 16:09:22: 19000000 INFO @ Wed, 22 Jul 2020 16:09:22: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:09:27: 20000000 INFO @ Wed, 22 Jul 2020 16:09:27: 31000000 INFO @ Wed, 22 Jul 2020 16:09:28: 22000000 INFO @ Wed, 22 Jul 2020 16:09:33: 21000000 INFO @ Wed, 22 Jul 2020 16:09:33: 32000000 INFO @ Wed, 22 Jul 2020 16:09:34: 23000000 INFO @ Wed, 22 Jul 2020 16:09:38: 22000000 INFO @ Wed, 22 Jul 2020 16:09:39: 33000000 INFO @ Wed, 22 Jul 2020 16:09:41: 24000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:09:44: 23000000 INFO @ Wed, 22 Jul 2020 16:09:44: 34000000 INFO @ Wed, 22 Jul 2020 16:09:48: 25000000 INFO @ Wed, 22 Jul 2020 16:09:50: 24000000 INFO @ Wed, 22 Jul 2020 16:09:50: 35000000 INFO @ Wed, 22 Jul 2020 16:09:54: 26000000 INFO @ Wed, 22 Jul 2020 16:09:55: 25000000 INFO @ Wed, 22 Jul 2020 16:09:56: 36000000 INFO @ Wed, 22 Jul 2020 16:10:01: 26000000 INFO @ Wed, 22 Jul 2020 16:10:01: 27000000 INFO @ Wed, 22 Jul 2020 16:10:02: 37000000 INFO @ Wed, 22 Jul 2020 16:10:06: 27000000 INFO @ Wed, 22 Jul 2020 16:10:07: 38000000 INFO @ Wed, 22 Jul 2020 16:10:08: 28000000 INFO @ Wed, 22 Jul 2020 16:10:12: 28000000 INFO @ Wed, 22 Jul 2020 16:10:13: 39000000 INFO @ Wed, 22 Jul 2020 16:10:13: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:10:13: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:10:13: #1 total tags in treatment: 19272243 INFO @ Wed, 22 Jul 2020 16:10:13: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:10:13: #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 16:10:14: #1 tags after filtering in treatment: 12386638 INFO @ Wed, 22 Jul 2020 16:10:14: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 16:10:14: #1 finished! INFO @ Wed, 22 Jul 2020 16:10:14: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:10:14: 29000000 INFO @ Wed, 22 Jul 2020 16:10:14: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:10:14: 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 16:10:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.05_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/SRX8639540/SRX8639540.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:10:18: 29000000 INFO @ Wed, 22 Jul 2020 16:10:21: 30000000 INFO @ Wed, 22 Jul 2020 16:10:23: 30000000 INFO @ Wed, 22 Jul 2020 16:10:27: 31000000 INFO @ Wed, 22 Jul 2020 16:10:29: 31000000 INFO @ Wed, 22 Jul 2020 16:10:34: 32000000 INFO @ Wed, 22 Jul 2020 16:10:35: 32000000 INFO @ Wed, 22 Jul 2020 16:10:40: 33000000 INFO @ Wed, 22 Jul 2020 16:10:41: 33000000 INFO @ Wed, 22 Jul 2020 16:10:47: 34000000 INFO @ Wed, 22 Jul 2020 16:10:48: 34000000 INFO @ Wed, 22 Jul 2020 16:10:54: 35000000 INFO @ Wed, 22 Jul 2020 16:10:55: 35000000 INFO @ Wed, 22 Jul 2020 16:11:00: 36000000 INFO @ Wed, 22 Jul 2020 16:11:01: 36000000 INFO @ Wed, 22 Jul 2020 16:11:07: 37000000 INFO @ Wed, 22 Jul 2020 16:11:08: 37000000 INFO @ Wed, 22 Jul 2020 16:11:15: 38000000 INFO @ Wed, 22 Jul 2020 16:11:15: 38000000 INFO @ Wed, 22 Jul 2020 16:11:22: 39000000 INFO @ Wed, 22 Jul 2020 16:11:22: 39000000 INFO @ Wed, 22 Jul 2020 16:11:22: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:11:22: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:11:22: #1 total tags in treatment: 19272243 INFO @ Wed, 22 Jul 2020 16:11:22: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:11:22: #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 16:11:22: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:11:22: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:11:22: #1 total tags in treatment: 19272243 INFO @ Wed, 22 Jul 2020 16:11:22: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:11:22: #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 16:11:23: #1 tags after filtering in treatment: 12386638 INFO @ Wed, 22 Jul 2020 16:11:23: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 16:11:23: #1 finished! INFO @ Wed, 22 Jul 2020 16:11:23: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:11:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:11:23: #1 tags after filtering in treatment: 12386638 INFO @ Wed, 22 Jul 2020 16:11:23: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 16:11:23: #1 finished! INFO @ Wed, 22 Jul 2020 16:11:23: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:11:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:11:23: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:11:23: 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 16:11:23: Process for pairing-model is terminated! INFO @ Wed, 22 Jul 2020 16:11:24: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:11:24: 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 16:11:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.20_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/SRX8639540/SRX8639540.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.10_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/SRX8639540/SRX8639540.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639540/SRX8639540.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling