Job ID = 7117686 SRX = SRX8639549 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:42:57 prefetch.2.10.7: 1) Downloading 'SRR12116987'... 2020-07-22T06:42:57 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:45:15 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:45:15 prefetch.2.10.7: 1) 'SRR12116987' was downloaded successfully 2020-07-22T06:45:15 prefetch.2.10.7: 'SRR12116987' has 0 unresolved dependencies Read 22252921 spots for SRR12116987/SRR12116987.sra Written 22252921 spots for SRR12116987/SRR12116987.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: 00:11:22 22252921 reads; of these: 22252921 (100.00%) were paired; of these: 2880189 (12.94%) aligned concordantly 0 times 17047428 (76.61%) aligned concordantly exactly 1 time 2325304 (10.45%) aligned concordantly >1 times ---- 2880189 pairs aligned concordantly 0 times; of these: 259481 (9.01%) aligned discordantly 1 time ---- 2620708 pairs aligned 0 times concordantly or discordantly; of these: 5241416 mates make up the pairs; of these: 4885516 (93.21%) aligned 0 times 242142 (4.62%) aligned exactly 1 time 113758 (2.17%) aligned >1 times 89.02% overall alignment rate Time searching: 00:11:22 Overall time: 00:11:22 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] 345335 / 19604680 = 0.0176 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 16:06:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.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 16:06:50: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:06:50: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:06:56: 1000000 INFO @ Wed, 22 Jul 2020 16:07:01: 2000000 INFO @ Wed, 22 Jul 2020 16:07:06: 3000000 INFO @ Wed, 22 Jul 2020 16:07:11: 4000000 INFO @ Wed, 22 Jul 2020 16:07:16: 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 16:07:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.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 16:07:20: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:07:20: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:07:22: 6000000 INFO @ Wed, 22 Jul 2020 16:07:25: 1000000 INFO @ Wed, 22 Jul 2020 16:07:27: 7000000 INFO @ Wed, 22 Jul 2020 16:07:30: 2000000 INFO @ Wed, 22 Jul 2020 16:07:33: 8000000 INFO @ Wed, 22 Jul 2020 16:07:35: 3000000 INFO @ Wed, 22 Jul 2020 16:07:38: 9000000 INFO @ Wed, 22 Jul 2020 16:07:39: 4000000 INFO @ Wed, 22 Jul 2020 16:07:44: 5000000 INFO @ Wed, 22 Jul 2020 16:07:44: 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 16:07:49: 6000000 INFO @ Wed, 22 Jul 2020 16:07:50: 11000000 INFO @ Wed, 22 Jul 2020 16:07:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.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 16:07:51: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:07:51: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:07:53: 7000000 INFO @ Wed, 22 Jul 2020 16:07:56: 12000000 INFO @ Wed, 22 Jul 2020 16:07:57: 1000000 INFO @ Wed, 22 Jul 2020 16:07:58: 8000000 INFO @ Wed, 22 Jul 2020 16:08:02: 13000000 INFO @ Wed, 22 Jul 2020 16:08:03: 9000000 INFO @ Wed, 22 Jul 2020 16:08:04: 2000000 INFO @ Wed, 22 Jul 2020 16:08:08: 10000000 INFO @ Wed, 22 Jul 2020 16:08:09: 14000000 INFO @ Wed, 22 Jul 2020 16:08:10: 3000000 INFO @ Wed, 22 Jul 2020 16:08:12: 11000000 INFO @ Wed, 22 Jul 2020 16:08:15: 15000000 INFO @ Wed, 22 Jul 2020 16:08:17: 4000000 INFO @ Wed, 22 Jul 2020 16:08:17: 12000000 INFO @ Wed, 22 Jul 2020 16:08:21: 16000000 INFO @ Wed, 22 Jul 2020 16:08:22: 13000000 INFO @ Wed, 22 Jul 2020 16:08:23: 5000000 INFO @ Wed, 22 Jul 2020 16:08:27: 14000000 INFO @ Wed, 22 Jul 2020 16:08:28: 17000000 INFO @ Wed, 22 Jul 2020 16:08:29: 6000000 INFO @ Wed, 22 Jul 2020 16:08:32: 15000000 INFO @ Wed, 22 Jul 2020 16:08:33: 18000000 INFO @ Wed, 22 Jul 2020 16:08:34: 7000000 INFO @ Wed, 22 Jul 2020 16:08:37: 16000000 INFO @ Wed, 22 Jul 2020 16:08:39: 19000000 INFO @ Wed, 22 Jul 2020 16:08:40: 8000000 INFO @ Wed, 22 Jul 2020 16:08:42: 17000000 INFO @ Wed, 22 Jul 2020 16:08:44: 20000000 INFO @ Wed, 22 Jul 2020 16:08:45: 9000000 INFO @ Wed, 22 Jul 2020 16:08:46: 18000000 INFO @ Wed, 22 Jul 2020 16:08:49: 21000000 INFO @ Wed, 22 Jul 2020 16:08:51: 10000000 INFO @ Wed, 22 Jul 2020 16:08:51: 19000000 INFO @ Wed, 22 Jul 2020 16:08:54: 22000000 INFO @ Wed, 22 Jul 2020 16:08:56: 20000000 INFO @ Wed, 22 Jul 2020 16:08:56: 11000000 INFO @ Wed, 22 Jul 2020 16:09:00: 23000000 INFO @ Wed, 22 Jul 2020 16:09:00: 21000000 INFO @ Wed, 22 Jul 2020 16:09:02: 12000000 INFO @ Wed, 22 Jul 2020 16:09:05: 24000000 INFO @ Wed, 22 Jul 2020 16:09:05: 22000000 INFO @ Wed, 22 Jul 2020 16:09:07: 13000000 INFO @ Wed, 22 Jul 2020 16:09:10: 23000000 INFO @ Wed, 22 Jul 2020 16:09:10: 25000000 INFO @ Wed, 22 Jul 2020 16:09:13: 14000000 INFO @ Wed, 22 Jul 2020 16:09:14: 24000000 INFO @ Wed, 22 Jul 2020 16:09:16: 26000000 INFO @ Wed, 22 Jul 2020 16:09:18: 15000000 INFO @ Wed, 22 Jul 2020 16:09:19: 25000000 INFO @ Wed, 22 Jul 2020 16:09:21: 27000000 INFO @ Wed, 22 Jul 2020 16:09:24: 16000000 INFO @ Wed, 22 Jul 2020 16:09:24: 26000000 INFO @ Wed, 22 Jul 2020 16:09:26: 28000000 INFO @ Wed, 22 Jul 2020 16:09:28: 27000000 INFO @ Wed, 22 Jul 2020 16:09:29: 17000000 INFO @ Wed, 22 Jul 2020 16:09:31: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:09:33: 28000000 INFO @ Wed, 22 Jul 2020 16:09:35: 18000000 INFO @ Wed, 22 Jul 2020 16:09:36: 30000000 INFO @ Wed, 22 Jul 2020 16:09:38: 29000000 INFO @ Wed, 22 Jul 2020 16:09:40: 19000000 INFO @ Wed, 22 Jul 2020 16:09:41: 31000000 INFO @ Wed, 22 Jul 2020 16:09:42: 30000000 INFO @ Wed, 22 Jul 2020 16:09:45: 20000000 INFO @ Wed, 22 Jul 2020 16:09:46: 32000000 INFO @ Wed, 22 Jul 2020 16:09:47: 31000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:09:51: 21000000 INFO @ Wed, 22 Jul 2020 16:09:51: 32000000 INFO @ Wed, 22 Jul 2020 16:09:52: 33000000 INFO @ Wed, 22 Jul 2020 16:09:56: 33000000 INFO @ Wed, 22 Jul 2020 16:09:56: 22000000 INFO @ Wed, 22 Jul 2020 16:09:57: 34000000 INFO @ Wed, 22 Jul 2020 16:10:01: 34000000 INFO @ Wed, 22 Jul 2020 16:10:01: 23000000 INFO @ Wed, 22 Jul 2020 16:10:02: 35000000 INFO @ Wed, 22 Jul 2020 16:10:05: 35000000 INFO @ Wed, 22 Jul 2020 16:10:07: 24000000 INFO @ Wed, 22 Jul 2020 16:10:07: 36000000 INFO @ Wed, 22 Jul 2020 16:10:10: 36000000 INFO @ Wed, 22 Jul 2020 16:10:12: 25000000 INFO @ Wed, 22 Jul 2020 16:10:12: 37000000 INFO @ Wed, 22 Jul 2020 16:10:14: 37000000 INFO @ Wed, 22 Jul 2020 16:10:17: 38000000 INFO @ Wed, 22 Jul 2020 16:10:17: 26000000 INFO @ Wed, 22 Jul 2020 16:10:19: 38000000 INFO @ Wed, 22 Jul 2020 16:10:22: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:10:22: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:10:22: #1 total tags in treatment: 19027855 INFO @ Wed, 22 Jul 2020 16:10:22: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:10:22: #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 16:10:23: 27000000 INFO @ Wed, 22 Jul 2020 16:10:23: #1 tags after filtering in treatment: 12329292 INFO @ Wed, 22 Jul 2020 16:10:23: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Jul 2020 16:10:23: #1 finished! INFO @ Wed, 22 Jul 2020 16:10:23: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:10:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:10:23: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:10:23: 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 16:10:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.05_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/SRX8639549/SRX8639549.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:10:24: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:10:24: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:10:24: #1 total tags in treatment: 19027855 INFO @ Wed, 22 Jul 2020 16:10:24: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:10:24: #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 16:10:24: #1 tags after filtering in treatment: 12329292 INFO @ Wed, 22 Jul 2020 16:10:24: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Jul 2020 16:10:24: #1 finished! INFO @ Wed, 22 Jul 2020 16:10:24: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:10:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:10:25: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:10:25: 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 16:10:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.10_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/SRX8639549/SRX8639549.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:10:28: 28000000 INFO @ Wed, 22 Jul 2020 16:10:33: 29000000 INFO @ Wed, 22 Jul 2020 16:10:38: 30000000 INFO @ Wed, 22 Jul 2020 16:10:43: 31000000 INFO @ Wed, 22 Jul 2020 16:10:48: 32000000 INFO @ Wed, 22 Jul 2020 16:10:53: 33000000 INFO @ Wed, 22 Jul 2020 16:10:58: 34000000 INFO @ Wed, 22 Jul 2020 16:11:03: 35000000 INFO @ Wed, 22 Jul 2020 16:11:08: 36000000 INFO @ Wed, 22 Jul 2020 16:11:13: 37000000 INFO @ Wed, 22 Jul 2020 16:11:19: 38000000 INFO @ Wed, 22 Jul 2020 16:11:24: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:11:24: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:11:24: #1 total tags in treatment: 19027855 INFO @ Wed, 22 Jul 2020 16:11:24: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:11:24: #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 16:11:24: #1 tags after filtering in treatment: 12329292 INFO @ Wed, 22 Jul 2020 16:11:24: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Jul 2020 16:11:24: #1 finished! INFO @ Wed, 22 Jul 2020 16:11:24: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:11:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:11:25: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:11:25: 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 16:11:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.20_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/SRX8639549/SRX8639549.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639549/SRX8639549.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling