Job ID = 7115714 SRX = SRX8639457 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:12:09 prefetch.2.10.7: 1) Downloading 'SRR12117029'... 2020-07-22T06:12:09 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:14:00 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:14:00 prefetch.2.10.7: 1) 'SRR12117029' was downloaded successfully 2020-07-22T06:14:00 prefetch.2.10.7: 'SRR12117029' has 0 unresolved dependencies Read 21889130 spots for SRR12117029/SRR12117029.sra Written 21889130 spots for SRR12117029/SRR12117029.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: 00:09:43 21889130 reads; of these: 21889130 (100.00%) were paired; of these: 4766165 (21.77%) aligned concordantly 0 times 15086343 (68.92%) aligned concordantly exactly 1 time 2036622 (9.30%) aligned concordantly >1 times ---- 4766165 pairs aligned concordantly 0 times; of these: 567983 (11.92%) aligned discordantly 1 time ---- 4198182 pairs aligned 0 times concordantly or discordantly; of these: 8396364 mates make up the pairs; of these: 7935196 (94.51%) aligned 0 times 233189 (2.78%) aligned exactly 1 time 227979 (2.72%) aligned >1 times 81.87% overall alignment rate Time searching: 00:09:43 Overall time: 00:09:43 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] 287179 / 17607746 = 0.0163 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 15:32:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.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 15:32:36: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:32:36: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:32:41: 1000000 INFO @ Wed, 22 Jul 2020 15:32:46: 2000000 INFO @ Wed, 22 Jul 2020 15:32:52: 3000000 INFO @ Wed, 22 Jul 2020 15:32:57: 4000000 INFO @ Wed, 22 Jul 2020 15:33:02: 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 15:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.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 15:33:06: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:33:06: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:33:07: 6000000 INFO @ Wed, 22 Jul 2020 15:33:11: 1000000 INFO @ Wed, 22 Jul 2020 15:33:13: 7000000 INFO @ Wed, 22 Jul 2020 15:33:16: 2000000 INFO @ Wed, 22 Jul 2020 15:33:18: 8000000 INFO @ Wed, 22 Jul 2020 15:33:21: 3000000 INFO @ Wed, 22 Jul 2020 15:33:23: 9000000 INFO @ Wed, 22 Jul 2020 15:33:26: 4000000 INFO @ Wed, 22 Jul 2020 15:33:28: 10000000 INFO @ Wed, 22 Jul 2020 15:33:31: 5000000 INFO @ Wed, 22 Jul 2020 15:33:33: 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 15:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.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 15:33:36: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:33:36: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:33:36: 6000000 INFO @ Wed, 22 Jul 2020 15:33:38: 12000000 INFO @ Wed, 22 Jul 2020 15:33:41: 1000000 INFO @ Wed, 22 Jul 2020 15:33:42: 7000000 INFO @ Wed, 22 Jul 2020 15:33:44: 13000000 INFO @ Wed, 22 Jul 2020 15:33:46: 2000000 INFO @ Wed, 22 Jul 2020 15:33:47: 8000000 INFO @ Wed, 22 Jul 2020 15:33:49: 14000000 INFO @ Wed, 22 Jul 2020 15:33:51: 3000000 INFO @ Wed, 22 Jul 2020 15:33:52: 9000000 INFO @ Wed, 22 Jul 2020 15:33:55: 15000000 INFO @ Wed, 22 Jul 2020 15:33:56: 4000000 INFO @ Wed, 22 Jul 2020 15:33:57: 10000000 INFO @ Wed, 22 Jul 2020 15:34:00: 16000000 INFO @ Wed, 22 Jul 2020 15:34:01: 5000000 INFO @ Wed, 22 Jul 2020 15:34:01: 11000000 INFO @ Wed, 22 Jul 2020 15:34:05: 17000000 INFO @ Wed, 22 Jul 2020 15:34:05: 6000000 INFO @ Wed, 22 Jul 2020 15:34:06: 12000000 INFO @ Wed, 22 Jul 2020 15:34:10: 7000000 INFO @ Wed, 22 Jul 2020 15:34:10: 18000000 INFO @ Wed, 22 Jul 2020 15:34:12: 13000000 INFO @ Wed, 22 Jul 2020 15:34:15: 8000000 INFO @ Wed, 22 Jul 2020 15:34:15: 19000000 INFO @ Wed, 22 Jul 2020 15:34:17: 14000000 INFO @ Wed, 22 Jul 2020 15:34:19: 9000000 INFO @ Wed, 22 Jul 2020 15:34:21: 20000000 INFO @ Wed, 22 Jul 2020 15:34:22: 15000000 INFO @ Wed, 22 Jul 2020 15:34:24: 10000000 INFO @ Wed, 22 Jul 2020 15:34:26: 21000000 INFO @ Wed, 22 Jul 2020 15:34:26: 16000000 INFO @ Wed, 22 Jul 2020 15:34:28: 11000000 INFO @ Wed, 22 Jul 2020 15:34:31: 22000000 INFO @ Wed, 22 Jul 2020 15:34:31: 17000000 INFO @ Wed, 22 Jul 2020 15:34:33: 12000000 INFO @ Wed, 22 Jul 2020 15:34:36: 23000000 INFO @ Wed, 22 Jul 2020 15:34:36: 18000000 INFO @ Wed, 22 Jul 2020 15:34:38: 13000000 INFO @ Wed, 22 Jul 2020 15:34:41: 19000000 INFO @ Wed, 22 Jul 2020 15:34:41: 24000000 INFO @ Wed, 22 Jul 2020 15:34:43: 14000000 INFO @ Wed, 22 Jul 2020 15:34:46: 20000000 INFO @ Wed, 22 Jul 2020 15:34:46: 25000000 INFO @ Wed, 22 Jul 2020 15:34:47: 15000000 INFO @ Wed, 22 Jul 2020 15:34:51: 21000000 INFO @ Wed, 22 Jul 2020 15:34:52: 26000000 INFO @ Wed, 22 Jul 2020 15:34:52: 16000000 INFO @ Wed, 22 Jul 2020 15:34:56: 22000000 INFO @ Wed, 22 Jul 2020 15:34:57: 17000000 INFO @ Wed, 22 Jul 2020 15:34:57: 27000000 INFO @ Wed, 22 Jul 2020 15:35:01: 23000000 INFO @ Wed, 22 Jul 2020 15:35:01: 18000000 INFO @ Wed, 22 Jul 2020 15:35:02: 28000000 INFO @ Wed, 22 Jul 2020 15:35:05: 24000000 INFO @ Wed, 22 Jul 2020 15:35:06: 19000000 INFO @ Wed, 22 Jul 2020 15:35:07: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 15:35:10: 25000000 INFO @ Wed, 22 Jul 2020 15:35:11: 20000000 INFO @ Wed, 22 Jul 2020 15:35:12: 30000000 INFO @ Wed, 22 Jul 2020 15:35:15: 26000000 INFO @ Wed, 22 Jul 2020 15:35:16: 21000000 INFO @ Wed, 22 Jul 2020 15:35:17: 31000000 INFO @ Wed, 22 Jul 2020 15:35:20: 27000000 INFO @ Wed, 22 Jul 2020 15:35:20: 22000000 INFO @ Wed, 22 Jul 2020 15:35:23: 32000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 15:35:25: 23000000 INFO @ Wed, 22 Jul 2020 15:35:25: 28000000 INFO @ Wed, 22 Jul 2020 15:35:28: 33000000 INFO @ Wed, 22 Jul 2020 15:35:30: 24000000 INFO @ Wed, 22 Jul 2020 15:35:30: 29000000 INFO @ Wed, 22 Jul 2020 15:35:33: 34000000 INFO @ Wed, 22 Jul 2020 15:35:34: 25000000 INFO @ Wed, 22 Jul 2020 15:35:35: 30000000 INFO @ Wed, 22 Jul 2020 15:35:38: 35000000 INFO @ Wed, 22 Jul 2020 15:35:39: 26000000 INFO @ Wed, 22 Jul 2020 15:35:39: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 15:35:39: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 15:35:39: #1 total tags in treatment: 16838745 INFO @ Wed, 22 Jul 2020 15:35:39: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:35:39: #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 15:35:40: 31000000 INFO @ Wed, 22 Jul 2020 15:35:40: #1 tags after filtering in treatment: 11358619 INFO @ Wed, 22 Jul 2020 15:35:40: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Jul 2020 15:35:40: #1 finished! INFO @ Wed, 22 Jul 2020 15:35:40: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:35:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:35:40: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 15:35:40: 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 15:35:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.05_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/SRX8639457/SRX8639457.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:35:44: 27000000 INFO @ Wed, 22 Jul 2020 15:35:44: 32000000 INFO @ Wed, 22 Jul 2020 15:35:48: 28000000 INFO @ Wed, 22 Jul 2020 15:35:49: 33000000 INFO @ Wed, 22 Jul 2020 15:35:53: 29000000 INFO @ Wed, 22 Jul 2020 15:35:54: 34000000 INFO @ Wed, 22 Jul 2020 15:35:58: 30000000 INFO @ Wed, 22 Jul 2020 15:35:58: 35000000 INFO @ Wed, 22 Jul 2020 15:36:00: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 15:36:00: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 15:36:00: #1 total tags in treatment: 16838745 INFO @ Wed, 22 Jul 2020 15:36:00: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:36:00: #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 15:36:00: #1 tags after filtering in treatment: 11358619 INFO @ Wed, 22 Jul 2020 15:36:00: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Jul 2020 15:36:00: #1 finished! INFO @ Wed, 22 Jul 2020 15:36:00: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:36:01: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 15:36:01: 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 15:36:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.10_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/SRX8639457/SRX8639457.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:36:02: 31000000 INFO @ Wed, 22 Jul 2020 15:36:07: 32000000 INFO @ Wed, 22 Jul 2020 15:36:11: 33000000 INFO @ Wed, 22 Jul 2020 15:36:16: 34000000 INFO @ Wed, 22 Jul 2020 15:36:20: 35000000 INFO @ Wed, 22 Jul 2020 15:36:21: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 15:36:21: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 15:36:21: #1 total tags in treatment: 16838745 INFO @ Wed, 22 Jul 2020 15:36:21: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:36:21: #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 15:36:22: #1 tags after filtering in treatment: 11358619 INFO @ Wed, 22 Jul 2020 15:36:22: #1 Redundant rate of treatment: 0.33 INFO @ Wed, 22 Jul 2020 15:36:22: #1 finished! INFO @ Wed, 22 Jul 2020 15:36:22: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:36:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:36:22: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 15:36:22: 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 15:36:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.20_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/SRX8639457/SRX8639457.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639457/SRX8639457.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling