Job ID = 7117664 SRX = SRX8639547 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:42:28 prefetch.2.10.7: 1) Downloading 'SRR12116985'... 2020-07-22T06:42:28 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:44:45 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:44:45 prefetch.2.10.7: 1) 'SRR12116985' was downloaded successfully 2020-07-22T06:44:45 prefetch.2.10.7: 'SRR12116985' has 0 unresolved dependencies Read 25010349 spots for SRR12116985/SRR12116985.sra Written 25010349 spots for SRR12116985/SRR12116985.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: 00:11:06 25010349 reads; of these: 25010349 (100.00%) were paired; of these: 4378105 (17.51%) aligned concordantly 0 times 18175839 (72.67%) aligned concordantly exactly 1 time 2456405 (9.82%) aligned concordantly >1 times ---- 4378105 pairs aligned concordantly 0 times; of these: 273444 (6.25%) aligned discordantly 1 time ---- 4104661 pairs aligned 0 times concordantly or discordantly; of these: 8209322 mates make up the pairs; of these: 7968883 (97.07%) aligned 0 times 142649 (1.74%) aligned exactly 1 time 97790 (1.19%) aligned >1 times 84.07% overall alignment rate Time searching: 00:11:06 Overall time: 00:11:06 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] 395810 / 20878620 = 0.0190 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 16:05:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.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 16:05:46: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:05:46: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:05:51: 1000000 INFO @ Wed, 22 Jul 2020 16:05:56: 2000000 INFO @ Wed, 22 Jul 2020 16:06:00: 3000000 INFO @ Wed, 22 Jul 2020 16:06:04: 4000000 INFO @ Wed, 22 Jul 2020 16:06:08: 5000000 INFO @ Wed, 22 Jul 2020 16:06:13: 6000000 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 16:06:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.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 16:06:16: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:06:16: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:06:17: 7000000 INFO @ Wed, 22 Jul 2020 16:06:21: 1000000 INFO @ Wed, 22 Jul 2020 16:06:22: 8000000 INFO @ Wed, 22 Jul 2020 16:06:25: 2000000 INFO @ Wed, 22 Jul 2020 16:06:26: 9000000 INFO @ Wed, 22 Jul 2020 16:06:30: 3000000 INFO @ Wed, 22 Jul 2020 16:06:31: 10000000 INFO @ Wed, 22 Jul 2020 16:06:35: 4000000 INFO @ Wed, 22 Jul 2020 16:06:35: 11000000 INFO @ Wed, 22 Jul 2020 16:06:39: 5000000 INFO @ Wed, 22 Jul 2020 16:06:40: 12000000 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 16:06:44: 13000000 INFO @ Wed, 22 Jul 2020 16:06:44: 6000000 INFO @ Wed, 22 Jul 2020 16:06:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.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 16:06:46: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:06:46: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:06:49: 14000000 INFO @ Wed, 22 Jul 2020 16:06:49: 7000000 INFO @ Wed, 22 Jul 2020 16:06:51: 1000000 INFO @ Wed, 22 Jul 2020 16:06:53: 15000000 INFO @ Wed, 22 Jul 2020 16:06:54: 8000000 INFO @ Wed, 22 Jul 2020 16:06:55: 2000000 INFO @ Wed, 22 Jul 2020 16:06:58: 16000000 INFO @ Wed, 22 Jul 2020 16:06:58: 9000000 INFO @ Wed, 22 Jul 2020 16:07:00: 3000000 INFO @ Wed, 22 Jul 2020 16:07:02: 17000000 INFO @ Wed, 22 Jul 2020 16:07:03: 10000000 INFO @ Wed, 22 Jul 2020 16:07:05: 4000000 INFO @ Wed, 22 Jul 2020 16:07:07: 18000000 INFO @ Wed, 22 Jul 2020 16:07:08: 11000000 INFO @ Wed, 22 Jul 2020 16:07:09: 5000000 INFO @ Wed, 22 Jul 2020 16:07:11: 19000000 INFO @ Wed, 22 Jul 2020 16:07:12: 12000000 INFO @ Wed, 22 Jul 2020 16:07:14: 6000000 INFO @ Wed, 22 Jul 2020 16:07:16: 20000000 INFO @ Wed, 22 Jul 2020 16:07:17: 13000000 INFO @ Wed, 22 Jul 2020 16:07:19: 7000000 INFO @ Wed, 22 Jul 2020 16:07:20: 21000000 INFO @ Wed, 22 Jul 2020 16:07:21: 14000000 INFO @ Wed, 22 Jul 2020 16:07:23: 8000000 INFO @ Wed, 22 Jul 2020 16:07:25: 22000000 INFO @ Wed, 22 Jul 2020 16:07:26: 15000000 INFO @ Wed, 22 Jul 2020 16:07:28: 9000000 INFO @ Wed, 22 Jul 2020 16:07:29: 23000000 INFO @ Wed, 22 Jul 2020 16:07:31: 16000000 INFO @ Wed, 22 Jul 2020 16:07:32: 10000000 INFO @ Wed, 22 Jul 2020 16:07:33: 24000000 INFO @ Wed, 22 Jul 2020 16:07:35: 17000000 INFO @ Wed, 22 Jul 2020 16:07:37: 11000000 INFO @ Wed, 22 Jul 2020 16:07:38: 25000000 INFO @ Wed, 22 Jul 2020 16:07:40: 18000000 INFO @ Wed, 22 Jul 2020 16:07:42: 12000000 INFO @ Wed, 22 Jul 2020 16:07:42: 26000000 INFO @ Wed, 22 Jul 2020 16:07:44: 19000000 INFO @ Wed, 22 Jul 2020 16:07:46: 13000000 INFO @ Wed, 22 Jul 2020 16:07:47: 27000000 INFO @ Wed, 22 Jul 2020 16:07:49: 20000000 INFO @ Wed, 22 Jul 2020 16:07:51: 14000000 INFO @ Wed, 22 Jul 2020 16:07:51: 28000000 INFO @ Wed, 22 Jul 2020 16:07:53: 21000000 INFO @ Wed, 22 Jul 2020 16:07:55: 15000000 INFO @ Wed, 22 Jul 2020 16:07:56: 29000000 INFO @ Wed, 22 Jul 2020 16:07:58: 22000000 INFO @ Wed, 22 Jul 2020 16:08:00: 16000000 INFO @ Wed, 22 Jul 2020 16:08:00: 30000000 INFO @ Wed, 22 Jul 2020 16:08:03: 23000000 INFO @ Wed, 22 Jul 2020 16:08:04: 17000000 INFO @ Wed, 22 Jul 2020 16:08:05: 31000000 INFO @ Wed, 22 Jul 2020 16:08:07: 24000000 INFO @ Wed, 22 Jul 2020 16:08:09: 18000000 INFO @ Wed, 22 Jul 2020 16:08:09: 32000000 INFO @ Wed, 22 Jul 2020 16:08:12: 25000000 INFO @ Wed, 22 Jul 2020 16:08:14: 19000000 INFO @ Wed, 22 Jul 2020 16:08:14: 33000000 INFO @ Wed, 22 Jul 2020 16:08:16: 26000000 INFO @ Wed, 22 Jul 2020 16:08:18: 20000000 INFO @ Wed, 22 Jul 2020 16:08:18: 34000000 INFO @ Wed, 22 Jul 2020 16:08:21: 27000000 INFO @ Wed, 22 Jul 2020 16:08:23: 21000000 INFO @ Wed, 22 Jul 2020 16:08:23: 35000000 INFO @ Wed, 22 Jul 2020 16:08:25: 28000000 INFO @ Wed, 22 Jul 2020 16:08:27: 22000000 INFO @ Wed, 22 Jul 2020 16:08:27: 36000000 INFO @ Wed, 22 Jul 2020 16:08:30: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:08:32: 37000000 INFO @ Wed, 22 Jul 2020 16:08:32: 23000000 INFO @ Wed, 22 Jul 2020 16:08:34: 30000000 INFO @ Wed, 22 Jul 2020 16:08:36: 38000000 INFO @ Wed, 22 Jul 2020 16:08:36: 24000000 INFO @ Wed, 22 Jul 2020 16:08:39: 31000000 INFO @ Wed, 22 Jul 2020 16:08:41: 39000000 INFO @ Wed, 22 Jul 2020 16:08:41: 25000000 INFO @ Wed, 22 Jul 2020 16:08:43: 32000000 INFO @ Wed, 22 Jul 2020 16:08:45: 40000000 INFO @ Wed, 22 Jul 2020 16:08:46: 26000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:08:48: 33000000 INFO @ Wed, 22 Jul 2020 16:08:50: 41000000 INFO @ Wed, 22 Jul 2020 16:08:50: 27000000 INFO @ Wed, 22 Jul 2020 16:08:51: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:08:51: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:08:51: #1 total tags in treatment: 20236682 INFO @ Wed, 22 Jul 2020 16:08:51: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:08:51: #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 16:08:52: #1 tags after filtering in treatment: 12864712 INFO @ Wed, 22 Jul 2020 16:08:52: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 16:08:52: #1 finished! INFO @ Wed, 22 Jul 2020 16:08:52: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:08:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:08:52: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:08:52: 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 16:08:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.05_peaks.narrowPeak: No such file or directory INFO @ Wed, 22 Jul 2020 16:08:52: 34000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:08:55: 28000000 INFO @ Wed, 22 Jul 2020 16:08:57: 35000000 INFO @ Wed, 22 Jul 2020 16:08:59: 29000000 INFO @ Wed, 22 Jul 2020 16:09:01: 36000000 INFO @ Wed, 22 Jul 2020 16:09:04: 30000000 INFO @ Wed, 22 Jul 2020 16:09:06: 37000000 INFO @ Wed, 22 Jul 2020 16:09:08: 31000000 INFO @ Wed, 22 Jul 2020 16:09:10: 38000000 INFO @ Wed, 22 Jul 2020 16:09:12: 32000000 INFO @ Wed, 22 Jul 2020 16:09:15: 39000000 INFO @ Wed, 22 Jul 2020 16:09:17: 33000000 INFO @ Wed, 22 Jul 2020 16:09:19: 40000000 INFO @ Wed, 22 Jul 2020 16:09:21: 34000000 INFO @ Wed, 22 Jul 2020 16:09:24: 41000000 INFO @ Wed, 22 Jul 2020 16:09:25: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:09:25: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:09:25: #1 total tags in treatment: 20236682 INFO @ Wed, 22 Jul 2020 16:09:25: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:09:25: #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 16:09:26: #1 tags after filtering in treatment: 12864712 INFO @ Wed, 22 Jul 2020 16:09:26: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 16:09:26: #1 finished! INFO @ Wed, 22 Jul 2020 16:09:26: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:09:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:09:26: 35000000 INFO @ Wed, 22 Jul 2020 16:09:26: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:09:26: 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 16:09:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.10_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/SRX8639547/SRX8639547.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:09:30: 36000000 INFO @ Wed, 22 Jul 2020 16:09:34: 37000000 INFO @ Wed, 22 Jul 2020 16:09:39: 38000000 INFO @ Wed, 22 Jul 2020 16:09:43: 39000000 INFO @ Wed, 22 Jul 2020 16:09:47: 40000000 INFO @ Wed, 22 Jul 2020 16:09:51: 41000000 INFO @ Wed, 22 Jul 2020 16:09:53: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:09:53: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:09:53: #1 total tags in treatment: 20236682 INFO @ Wed, 22 Jul 2020 16:09:53: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:09:53: #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 16:09:53: #1 tags after filtering in treatment: 12864712 INFO @ Wed, 22 Jul 2020 16:09:53: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Jul 2020 16:09:53: #1 finished! INFO @ Wed, 22 Jul 2020 16:09:53: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:09:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:09:54: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:09:54: 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 16:09:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.20_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/SRX8639547/SRX8639547.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639547/SRX8639547.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling