Job ID = 5791651 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:16:09 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 28,602,759 reads read : 57,205,518 reads written : 57,205,518 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:15:54 28602759 reads; of these: 28602759 (100.00%) were paired; of these: 691253 (2.42%) aligned concordantly 0 times 25025176 (87.49%) aligned concordantly exactly 1 time 2886330 (10.09%) aligned concordantly >1 times ---- 691253 pairs aligned concordantly 0 times; of these: 36638 (5.30%) aligned discordantly 1 time ---- 654615 pairs aligned 0 times concordantly or discordantly; of these: 1309230 mates make up the pairs; of these: 1049702 (80.18%) aligned 0 times 215002 (16.42%) aligned exactly 1 time 44526 (3.40%) aligned >1 times 98.17% overall alignment rate Time searching: 00:15:54 Overall time: 00:15:54 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] 4329612 / 27918245 = 0.1551 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 Apr 2020 10:49:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.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 Apr 2020 10:49:31: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:49:31: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:49:36: 1000000 INFO @ Wed, 22 Apr 2020 10:49:40: 2000000 INFO @ Wed, 22 Apr 2020 10:49:45: 3000000 INFO @ Wed, 22 Apr 2020 10:49:50: 4000000 INFO @ Wed, 22 Apr 2020 10:49:55: 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 Apr 2020 10:49:59: 6000000 INFO @ Wed, 22 Apr 2020 10:50:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.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 Apr 2020 10:50:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:50:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:50:04: 7000000 INFO @ Wed, 22 Apr 2020 10:50:07: 1000000 INFO @ Wed, 22 Apr 2020 10:50:10: 8000000 INFO @ Wed, 22 Apr 2020 10:50:14: 2000000 INFO @ Wed, 22 Apr 2020 10:50:15: 9000000 INFO @ Wed, 22 Apr 2020 10:50:20: 3000000 INFO @ Wed, 22 Apr 2020 10:50:21: 10000000 INFO @ Wed, 22 Apr 2020 10:50:26: 4000000 INFO @ Wed, 22 Apr 2020 10:50:26: 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 Apr 2020 10:50:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.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 Apr 2020 10:50:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:50:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:50:32: 12000000 INFO @ Wed, 22 Apr 2020 10:50:32: 5000000 INFO @ Wed, 22 Apr 2020 10:50:35: 1000000 INFO @ Wed, 22 Apr 2020 10:50:37: 13000000 INFO @ Wed, 22 Apr 2020 10:50:39: 6000000 INFO @ Wed, 22 Apr 2020 10:50:40: 2000000 INFO @ Wed, 22 Apr 2020 10:50:43: 14000000 INFO @ Wed, 22 Apr 2020 10:50:45: 7000000 INFO @ Wed, 22 Apr 2020 10:50:46: 3000000 INFO @ Wed, 22 Apr 2020 10:50:49: 15000000 INFO @ Wed, 22 Apr 2020 10:50:51: 8000000 INFO @ Wed, 22 Apr 2020 10:50:52: 4000000 INFO @ Wed, 22 Apr 2020 10:50:54: 16000000 INFO @ Wed, 22 Apr 2020 10:50:57: 5000000 INFO @ Wed, 22 Apr 2020 10:50:58: 9000000 INFO @ Wed, 22 Apr 2020 10:51:00: 17000000 INFO @ Wed, 22 Apr 2020 10:51:03: 6000000 INFO @ Wed, 22 Apr 2020 10:51:04: 10000000 INFO @ Wed, 22 Apr 2020 10:51:06: 18000000 INFO @ Wed, 22 Apr 2020 10:51:09: 7000000 INFO @ Wed, 22 Apr 2020 10:51:11: 11000000 INFO @ Wed, 22 Apr 2020 10:51:12: 19000000 INFO @ Wed, 22 Apr 2020 10:51:15: 8000000 INFO @ Wed, 22 Apr 2020 10:51:17: 12000000 INFO @ Wed, 22 Apr 2020 10:51:17: 20000000 INFO @ Wed, 22 Apr 2020 10:51:20: 9000000 INFO @ Wed, 22 Apr 2020 10:51:23: 21000000 INFO @ Wed, 22 Apr 2020 10:51:23: 13000000 INFO @ Wed, 22 Apr 2020 10:51:26: 10000000 INFO @ Wed, 22 Apr 2020 10:51:29: 22000000 INFO @ Wed, 22 Apr 2020 10:51:30: 14000000 INFO @ Wed, 22 Apr 2020 10:51:32: 11000000 INFO @ Wed, 22 Apr 2020 10:51:34: 23000000 INFO @ Wed, 22 Apr 2020 10:51:36: 15000000 INFO @ Wed, 22 Apr 2020 10:51:37: 12000000 INFO @ Wed, 22 Apr 2020 10:51:40: 24000000 INFO @ Wed, 22 Apr 2020 10:51:43: 16000000 INFO @ Wed, 22 Apr 2020 10:51:43: 13000000 INFO @ Wed, 22 Apr 2020 10:51:46: 25000000 INFO @ Wed, 22 Apr 2020 10:51:49: 14000000 INFO @ Wed, 22 Apr 2020 10:51:49: 17000000 INFO @ Wed, 22 Apr 2020 10:51:51: 26000000 INFO @ Wed, 22 Apr 2020 10:51:54: 15000000 INFO @ Wed, 22 Apr 2020 10:51:55: 18000000 INFO @ Wed, 22 Apr 2020 10:51:57: 27000000 INFO @ Wed, 22 Apr 2020 10:52:00: 16000000 INFO @ Wed, 22 Apr 2020 10:52:02: 19000000 INFO @ Wed, 22 Apr 2020 10:52:02: 28000000 INFO @ Wed, 22 Apr 2020 10:52:06: 17000000 INFO @ Wed, 22 Apr 2020 10:52:08: 29000000 INFO @ Wed, 22 Apr 2020 10:52:08: 20000000 INFO @ Wed, 22 Apr 2020 10:52:11: 18000000 INFO @ Wed, 22 Apr 2020 10:52:14: 30000000 INFO @ Wed, 22 Apr 2020 10:52:15: 21000000 INFO @ Wed, 22 Apr 2020 10:52:17: 19000000 INFO @ Wed, 22 Apr 2020 10:52:20: 31000000 INFO @ Wed, 22 Apr 2020 10:52:21: 22000000 INFO @ Wed, 22 Apr 2020 10:52:22: 20000000 INFO @ Wed, 22 Apr 2020 10:52:25: 32000000 INFO @ Wed, 22 Apr 2020 10:52:27: 23000000 INFO @ Wed, 22 Apr 2020 10:52:28: 21000000 INFO @ Wed, 22 Apr 2020 10:52:31: 33000000 INFO @ Wed, 22 Apr 2020 10:52:34: 22000000 INFO @ Wed, 22 Apr 2020 10:52:34: 24000000 INFO @ Wed, 22 Apr 2020 10:52:36: 34000000 INFO @ Wed, 22 Apr 2020 10:52:39: 23000000 INFO @ Wed, 22 Apr 2020 10:52:40: 25000000 INFO @ Wed, 22 Apr 2020 10:52:42: 35000000 INFO @ Wed, 22 Apr 2020 10:52:45: 24000000 INFO @ Wed, 22 Apr 2020 10:52:46: 26000000 INFO @ Wed, 22 Apr 2020 10:52:48: 36000000 INFO @ Wed, 22 Apr 2020 10:52:50: 25000000 INFO @ Wed, 22 Apr 2020 10:52:52: 27000000 INFO @ Wed, 22 Apr 2020 10:52:53: 37000000 INFO @ Wed, 22 Apr 2020 10:52:56: 26000000 INFO @ Wed, 22 Apr 2020 10:52:59: 28000000 INFO @ Wed, 22 Apr 2020 10:52:59: 38000000 INFO @ Wed, 22 Apr 2020 10:53:02: 27000000 INFO @ Wed, 22 Apr 2020 10:53:05: 39000000 INFO @ Wed, 22 Apr 2020 10:53:05: 29000000 INFO @ Wed, 22 Apr 2020 10:53:07: 28000000 INFO @ Wed, 22 Apr 2020 10:53:10: 40000000 INFO @ Wed, 22 Apr 2020 10:53:11: 30000000 INFO @ Wed, 22 Apr 2020 10:53:13: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:53:16: 41000000 INFO @ Wed, 22 Apr 2020 10:53:17: 31000000 INFO @ Wed, 22 Apr 2020 10:53:19: 30000000 INFO @ Wed, 22 Apr 2020 10:53:21: 42000000 INFO @ Wed, 22 Apr 2020 10:53:23: 32000000 INFO @ Wed, 22 Apr 2020 10:53:24: 31000000 INFO @ Wed, 22 Apr 2020 10:53:27: 43000000 INFO @ Wed, 22 Apr 2020 10:53:29: 33000000 INFO @ Wed, 22 Apr 2020 10:53:30: 32000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:53:33: 44000000 INFO @ Wed, 22 Apr 2020 10:53:35: 33000000 INFO @ Wed, 22 Apr 2020 10:53:36: 34000000 INFO @ Wed, 22 Apr 2020 10:53:38: 45000000 INFO @ Wed, 22 Apr 2020 10:53:41: 34000000 INFO @ Wed, 22 Apr 2020 10:53:42: 35000000 INFO @ Wed, 22 Apr 2020 10:53:44: 46000000 INFO @ Wed, 22 Apr 2020 10:53:47: 35000000 INFO @ Wed, 22 Apr 2020 10:53:48: 36000000 INFO @ Wed, 22 Apr 2020 10:53:50: 47000000 INFO @ Wed, 22 Apr 2020 10:53:52: 36000000 INFO @ Wed, 22 Apr 2020 10:53:52: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:53:52: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:53:52: #1 total tags in treatment: 23583043 INFO @ Wed, 22 Apr 2020 10:53:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:53:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:53:53: #1 tags after filtering in treatment: 12496507 INFO @ Wed, 22 Apr 2020 10:53:53: #1 Redundant rate of treatment: 0.47 INFO @ Wed, 22 Apr 2020 10:53:53: #1 finished! INFO @ Wed, 22 Apr 2020 10:53:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:53:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:53:54: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:53:54: 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 Apr 2020 10:53:54: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:53:54: 37000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.05_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/SRX7409615/SRX7409615.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:53:58: 37000000 INFO @ Wed, 22 Apr 2020 10:54:00: 38000000 INFO @ Wed, 22 Apr 2020 10:54:03: 38000000 INFO @ Wed, 22 Apr 2020 10:54:07: 39000000 INFO @ Wed, 22 Apr 2020 10:54:09: 39000000 INFO @ Wed, 22 Apr 2020 10:54:13: 40000000 INFO @ Wed, 22 Apr 2020 10:54:14: 40000000 INFO @ Wed, 22 Apr 2020 10:54:19: 41000000 INFO @ Wed, 22 Apr 2020 10:54:20: 41000000 INFO @ Wed, 22 Apr 2020 10:54:25: 42000000 INFO @ Wed, 22 Apr 2020 10:54:26: 42000000 INFO @ Wed, 22 Apr 2020 10:54:31: 43000000 INFO @ Wed, 22 Apr 2020 10:54:32: 43000000 INFO @ Wed, 22 Apr 2020 10:54:38: 44000000 INFO @ Wed, 22 Apr 2020 10:54:39: 44000000 INFO @ Wed, 22 Apr 2020 10:54:44: 45000000 INFO @ Wed, 22 Apr 2020 10:54:45: 45000000 INFO @ Wed, 22 Apr 2020 10:54:50: 46000000 INFO @ Wed, 22 Apr 2020 10:54:51: 46000000 INFO @ Wed, 22 Apr 2020 10:54:56: 47000000 INFO @ Wed, 22 Apr 2020 10:54:57: 47000000 INFO @ Wed, 22 Apr 2020 10:54:59: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:54:59: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:54:59: #1 total tags in treatment: 23583043 INFO @ Wed, 22 Apr 2020 10:54:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:54:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:55:00: #1 tags after filtering in treatment: 12496507 INFO @ Wed, 22 Apr 2020 10:55:00: #1 Redundant rate of treatment: 0.47 INFO @ Wed, 22 Apr 2020 10:55:00: #1 finished! INFO @ Wed, 22 Apr 2020 10:55:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:55:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:55:00: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:55:00: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:55:00: #1 total tags in treatment: 23583043 INFO @ Wed, 22 Apr 2020 10:55:00: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:55:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:55:01: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:55:01: 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 Apr 2020 10:55:01: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:55:01: #1 tags after filtering in treatment: 12496507 INFO @ Wed, 22 Apr 2020 10:55:01: #1 Redundant rate of treatment: 0.47 INFO @ Wed, 22 Apr 2020 10:55:01: #1 finished! INFO @ Wed, 22 Apr 2020 10:55:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:55:02: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:55:02: 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 Apr 2020 10:55:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.10_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/SRX7409615/SRX7409615.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.20_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/SRX7409615/SRX7409615.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409615/SRX7409615.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling