Job ID = 7117399 SRX = SRX8639504 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:38:25 prefetch.2.10.7: 1) Downloading 'SRR12117068'... 2020-07-22T06:38:25 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:44:28 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:44:28 prefetch.2.10.7: 1) 'SRR12117068' was downloaded successfully 2020-07-22T06:44:28 prefetch.2.10.7: 'SRR12117068' has 0 unresolved dependencies Read 30333341 spots for SRR12117068/SRR12117068.sra Written 30333341 spots for SRR12117068/SRR12117068.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: 00:14:58 30333341 reads; of these: 30333341 (100.00%) were paired; of these: 4277654 (14.10%) aligned concordantly 0 times 22639330 (74.64%) aligned concordantly exactly 1 time 3416357 (11.26%) aligned concordantly >1 times ---- 4277654 pairs aligned concordantly 0 times; of these: 345075 (8.07%) aligned discordantly 1 time ---- 3932579 pairs aligned 0 times concordantly or discordantly; of these: 7865158 mates make up the pairs; of these: 7322603 (93.10%) aligned 0 times 355814 (4.52%) aligned exactly 1 time 186741 (2.37%) aligned >1 times 87.93% overall alignment rate Time searching: 00:14:58 Overall time: 00:14:58 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 24 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] 737485 / 26241997 = 0.0281 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 16:12:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.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 16:12:13: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:12:13: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:12:18: 1000000 INFO @ Wed, 22 Jul 2020 16:12:24: 2000000 INFO @ Wed, 22 Jul 2020 16:12:29: 3000000 INFO @ Wed, 22 Jul 2020 16:12:35: 4000000 INFO @ Wed, 22 Jul 2020 16:12:41: 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 16:12:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.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 16:12:43: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:12:43: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:12:46: 6000000 INFO @ Wed, 22 Jul 2020 16:12:49: 1000000 INFO @ Wed, 22 Jul 2020 16:12:52: 7000000 INFO @ Wed, 22 Jul 2020 16:12:54: 2000000 INFO @ Wed, 22 Jul 2020 16:12:58: 8000000 INFO @ Wed, 22 Jul 2020 16:13:00: 3000000 INFO @ Wed, 22 Jul 2020 16:13:04: 9000000 INFO @ Wed, 22 Jul 2020 16:13:06: 4000000 INFO @ Wed, 22 Jul 2020 16:13:10: 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 16:13:12: 5000000 INFO @ Wed, 22 Jul 2020 16:13:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.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 16:13:13: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:13:13: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:13:16: 11000000 INFO @ Wed, 22 Jul 2020 16:13:18: 6000000 INFO @ Wed, 22 Jul 2020 16:13:18: 1000000 INFO @ Wed, 22 Jul 2020 16:13:22: 12000000 INFO @ Wed, 22 Jul 2020 16:13:24: 2000000 INFO @ Wed, 22 Jul 2020 16:13:24: 7000000 INFO @ Wed, 22 Jul 2020 16:13:29: 13000000 INFO @ Wed, 22 Jul 2020 16:13:29: 3000000 INFO @ Wed, 22 Jul 2020 16:13:30: 8000000 INFO @ Wed, 22 Jul 2020 16:13:34: 4000000 INFO @ Wed, 22 Jul 2020 16:13:34: 14000000 INFO @ Wed, 22 Jul 2020 16:13:36: 9000000 INFO @ Wed, 22 Jul 2020 16:13:39: 5000000 INFO @ Wed, 22 Jul 2020 16:13:40: 15000000 INFO @ Wed, 22 Jul 2020 16:13:42: 10000000 INFO @ Wed, 22 Jul 2020 16:13:45: 6000000 INFO @ Wed, 22 Jul 2020 16:13:46: 16000000 INFO @ Wed, 22 Jul 2020 16:13:48: 11000000 INFO @ Wed, 22 Jul 2020 16:13:50: 7000000 INFO @ Wed, 22 Jul 2020 16:13:52: 17000000 INFO @ Wed, 22 Jul 2020 16:13:54: 12000000 INFO @ Wed, 22 Jul 2020 16:13:55: 8000000 INFO @ Wed, 22 Jul 2020 16:13:58: 18000000 INFO @ Wed, 22 Jul 2020 16:14:00: 13000000 INFO @ Wed, 22 Jul 2020 16:14:01: 9000000 INFO @ Wed, 22 Jul 2020 16:14:04: 19000000 INFO @ Wed, 22 Jul 2020 16:14:06: 10000000 INFO @ Wed, 22 Jul 2020 16:14:06: 14000000 INFO @ Wed, 22 Jul 2020 16:14:10: 20000000 INFO @ Wed, 22 Jul 2020 16:14:11: 11000000 INFO @ Wed, 22 Jul 2020 16:14:12: 15000000 INFO @ Wed, 22 Jul 2020 16:14:16: 12000000 INFO @ Wed, 22 Jul 2020 16:14:16: 21000000 INFO @ Wed, 22 Jul 2020 16:14:18: 16000000 INFO @ Wed, 22 Jul 2020 16:14:22: 13000000 INFO @ Wed, 22 Jul 2020 16:14:22: 22000000 INFO @ Wed, 22 Jul 2020 16:14:25: 17000000 INFO @ Wed, 22 Jul 2020 16:14:27: 14000000 INFO @ Wed, 22 Jul 2020 16:14:28: 23000000 INFO @ Wed, 22 Jul 2020 16:14:31: 18000000 INFO @ Wed, 22 Jul 2020 16:14:32: 15000000 INFO @ Wed, 22 Jul 2020 16:14:34: 24000000 INFO @ Wed, 22 Jul 2020 16:14:37: 19000000 INFO @ Wed, 22 Jul 2020 16:14:37: 16000000 INFO @ Wed, 22 Jul 2020 16:14:40: 25000000 INFO @ Wed, 22 Jul 2020 16:14:42: 17000000 INFO @ Wed, 22 Jul 2020 16:14:43: 20000000 INFO @ Wed, 22 Jul 2020 16:14:46: 26000000 INFO @ Wed, 22 Jul 2020 16:14:47: 18000000 INFO @ Wed, 22 Jul 2020 16:14:49: 21000000 INFO @ Wed, 22 Jul 2020 16:14:52: 27000000 INFO @ Wed, 22 Jul 2020 16:14:53: 19000000 INFO @ Wed, 22 Jul 2020 16:14:55: 22000000 INFO @ Wed, 22 Jul 2020 16:14:58: 28000000 INFO @ Wed, 22 Jul 2020 16:14:58: 20000000 INFO @ Wed, 22 Jul 2020 16:15:02: 23000000 INFO @ Wed, 22 Jul 2020 16:15:03: 21000000 INFO @ Wed, 22 Jul 2020 16:15:04: 29000000 INFO @ Wed, 22 Jul 2020 16:15:08: 24000000 INFO @ Wed, 22 Jul 2020 16:15:08: 22000000 INFO @ Wed, 22 Jul 2020 16:15:10: 30000000 INFO @ Wed, 22 Jul 2020 16:15:14: 23000000 INFO @ Wed, 22 Jul 2020 16:15:14: 25000000 INFO @ Wed, 22 Jul 2020 16:15:16: 31000000 INFO @ Wed, 22 Jul 2020 16:15:19: 24000000 INFO @ Wed, 22 Jul 2020 16:15:20: 26000000 INFO @ Wed, 22 Jul 2020 16:15:22: 32000000 INFO @ Wed, 22 Jul 2020 16:15:24: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:15:26: 27000000 INFO @ Wed, 22 Jul 2020 16:15:28: 33000000 INFO @ Wed, 22 Jul 2020 16:15:29: 26000000 INFO @ Wed, 22 Jul 2020 16:15:32: 28000000 INFO @ Wed, 22 Jul 2020 16:15:34: 34000000 INFO @ Wed, 22 Jul 2020 16:15:35: 27000000 INFO @ Wed, 22 Jul 2020 16:15:38: 29000000 INFO @ Wed, 22 Jul 2020 16:15:40: 35000000 INFO @ Wed, 22 Jul 2020 16:15:40: 28000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:15:45: 30000000 INFO @ Wed, 22 Jul 2020 16:15:45: 29000000 INFO @ Wed, 22 Jul 2020 16:15:46: 36000000 INFO @ Wed, 22 Jul 2020 16:15:50: 30000000 INFO @ Wed, 22 Jul 2020 16:15:51: 31000000 INFO @ Wed, 22 Jul 2020 16:15:52: 37000000 INFO @ Wed, 22 Jul 2020 16:15:55: 31000000 INFO @ Wed, 22 Jul 2020 16:15:57: 32000000 INFO @ Wed, 22 Jul 2020 16:15:58: 38000000 INFO @ Wed, 22 Jul 2020 16:16:01: 32000000 INFO @ Wed, 22 Jul 2020 16:16:03: 33000000 INFO @ Wed, 22 Jul 2020 16:16:04: 39000000 INFO @ Wed, 22 Jul 2020 16:16:06: 33000000 INFO @ Wed, 22 Jul 2020 16:16:09: 34000000 INFO @ Wed, 22 Jul 2020 16:16:10: 40000000 INFO @ Wed, 22 Jul 2020 16:16:11: 34000000 INFO @ Wed, 22 Jul 2020 16:16:15: 35000000 INFO @ Wed, 22 Jul 2020 16:16:16: 41000000 INFO @ Wed, 22 Jul 2020 16:16:16: 35000000 INFO @ Wed, 22 Jul 2020 16:16:21: 36000000 INFO @ Wed, 22 Jul 2020 16:16:22: 42000000 INFO @ Wed, 22 Jul 2020 16:16:22: 36000000 INFO @ Wed, 22 Jul 2020 16:16:28: 43000000 INFO @ Wed, 22 Jul 2020 16:16:28: 37000000 INFO @ Wed, 22 Jul 2020 16:16:29: 37000000 INFO @ Wed, 22 Jul 2020 16:16:34: 44000000 INFO @ Wed, 22 Jul 2020 16:16:34: 38000000 INFO @ Wed, 22 Jul 2020 16:16:35: 38000000 INFO @ Wed, 22 Jul 2020 16:16:40: 45000000 INFO @ Wed, 22 Jul 2020 16:16:40: 39000000 INFO @ Wed, 22 Jul 2020 16:16:41: 39000000 INFO @ Wed, 22 Jul 2020 16:16:46: 46000000 INFO @ Wed, 22 Jul 2020 16:16:46: 40000000 INFO @ Wed, 22 Jul 2020 16:16:47: 40000000 INFO @ Wed, 22 Jul 2020 16:16:52: 47000000 INFO @ Wed, 22 Jul 2020 16:16:53: 41000000 INFO @ Wed, 22 Jul 2020 16:16:54: 41000000 INFO @ Wed, 22 Jul 2020 16:16:58: 48000000 INFO @ Wed, 22 Jul 2020 16:16:59: 42000000 INFO @ Wed, 22 Jul 2020 16:17:00: 42000000 INFO @ Wed, 22 Jul 2020 16:17:04: 49000000 INFO @ Wed, 22 Jul 2020 16:17:05: 43000000 INFO @ Wed, 22 Jul 2020 16:17:06: 43000000 INFO @ Wed, 22 Jul 2020 16:17:09: 50000000 INFO @ Wed, 22 Jul 2020 16:17:11: 44000000 INFO @ Wed, 22 Jul 2020 16:17:12: 44000000 INFO @ Wed, 22 Jul 2020 16:17:15: 51000000 INFO @ Wed, 22 Jul 2020 16:17:18: 45000000 INFO @ Wed, 22 Jul 2020 16:17:19: 45000000 INFO @ Wed, 22 Jul 2020 16:17:21: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:17:21: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:17:21: #1 total tags in treatment: 25319136 INFO @ Wed, 22 Jul 2020 16:17:21: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:17:21: #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 16:17:21: #1 tags after filtering in treatment: 14715286 INFO @ Wed, 22 Jul 2020 16:17:21: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Jul 2020 16:17:21: #1 finished! INFO @ Wed, 22 Jul 2020 16:17:21: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:17:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:17:22: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:17:22: 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 16:17:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.05_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/SRX8639504/SRX8639504.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:17:24: 46000000 INFO @ Wed, 22 Jul 2020 16:17:25: 46000000 INFO @ Wed, 22 Jul 2020 16:17:30: 47000000 INFO @ Wed, 22 Jul 2020 16:17:31: 47000000 INFO @ Wed, 22 Jul 2020 16:17:36: 48000000 INFO @ Wed, 22 Jul 2020 16:17:37: 48000000 INFO @ Wed, 22 Jul 2020 16:17:42: 49000000 INFO @ Wed, 22 Jul 2020 16:17:43: 49000000 INFO @ Wed, 22 Jul 2020 16:17:48: 50000000 INFO @ Wed, 22 Jul 2020 16:17:49: 50000000 INFO @ Wed, 22 Jul 2020 16:17:54: 51000000 INFO @ Wed, 22 Jul 2020 16:17:55: 51000000 INFO @ Wed, 22 Jul 2020 16:18:00: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:18:00: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:18:00: #1 total tags in treatment: 25319136 INFO @ Wed, 22 Jul 2020 16:18:00: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:18:00: #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 16:18:00: #1 tags after filtering in treatment: 14715286 INFO @ Wed, 22 Jul 2020 16:18:00: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Jul 2020 16:18:00: #1 finished! INFO @ Wed, 22 Jul 2020 16:18:00: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:18:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:18:01: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:18:01: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:18:01: #1 total tags in treatment: 25319136 INFO @ Wed, 22 Jul 2020 16:18:01: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:18:01: #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 16:18:01: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:18:01: 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 16:18:01: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.10_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/SRX8639504/SRX8639504.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:18:01: #1 tags after filtering in treatment: 14715286 INFO @ Wed, 22 Jul 2020 16:18:01: #1 Redundant rate of treatment: 0.42 INFO @ Wed, 22 Jul 2020 16:18:01: #1 finished! INFO @ Wed, 22 Jul 2020 16:18:01: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:18:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:18:02: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:18:02: 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 16:18:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.20_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/SRX8639504/SRX8639504.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639504/SRX8639504.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling