Job ID = 2010574 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:16:55 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 ) 2019-07-05T14:21:09 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 ) 2019-07-05T14:21:09 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 ) 2019-07-05T14:21:09 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 ) 2019-07-05T14:21:09 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 ) 2019-07-05T14:24:30 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 ) 2019-07-05T14:25:19 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 ) 2019-07-05T14:26:05 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 ) 2019-07-05T14:27:46 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 : 15,807,777 reads read : 31,615,554 reads written : 31,615,554 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: 00:14:03 15807777 reads; of these: 15807777 (100.00%) were paired; of these: 2711195 (17.15%) aligned concordantly 0 times 11155797 (70.57%) aligned concordantly exactly 1 time 1940785 (12.28%) aligned concordantly >1 times ---- 2711195 pairs aligned concordantly 0 times; of these: 207998 (7.67%) aligned discordantly 1 time ---- 2503197 pairs aligned 0 times concordantly or discordantly; of these: 5006394 mates make up the pairs; of these: 4761012 (95.10%) aligned 0 times 123272 (2.46%) aligned exactly 1 time 122110 (2.44%) aligned >1 times 84.94% overall alignment rate Time searching: 00:14:03 Overall time: 00:14:03 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 12 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] 563476 / 13288297 = 0.0424 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 23:56:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.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 @ Fri, 05 Jul 2019 23:56:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:56:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:56:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.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 @ Fri, 05 Jul 2019 23:56:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:56:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:56:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.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 @ Fri, 05 Jul 2019 23:56:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:56:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:57:04: 1000000 INFO @ Fri, 05 Jul 2019 23:57:07: 1000000 INFO @ Fri, 05 Jul 2019 23:57:08: 1000000 INFO @ Fri, 05 Jul 2019 23:57:10: 2000000 INFO @ Fri, 05 Jul 2019 23:57:16: 3000000 INFO @ Fri, 05 Jul 2019 23:57:16: 2000000 INFO @ Fri, 05 Jul 2019 23:57:16: 2000000 INFO @ Fri, 05 Jul 2019 23:57:22: 4000000 INFO @ Fri, 05 Jul 2019 23:57:24: 3000000 INFO @ Fri, 05 Jul 2019 23:57:25: 3000000 INFO @ Fri, 05 Jul 2019 23:57:28: 5000000 INFO @ Fri, 05 Jul 2019 23:57:32: 4000000 INFO @ Fri, 05 Jul 2019 23:57:34: 6000000 INFO @ Fri, 05 Jul 2019 23:57:35: 4000000 INFO @ Fri, 05 Jul 2019 23:57:39: 7000000 INFO @ Fri, 05 Jul 2019 23:57:40: 5000000 INFO @ Fri, 05 Jul 2019 23:57:44: 5000000 INFO @ Fri, 05 Jul 2019 23:57:45: 8000000 INFO @ Fri, 05 Jul 2019 23:57:49: 6000000 INFO @ Fri, 05 Jul 2019 23:57:51: 9000000 INFO @ Fri, 05 Jul 2019 23:57:53: 6000000 INFO @ Fri, 05 Jul 2019 23:57:57: 7000000 INFO @ Fri, 05 Jul 2019 23:57:57: 10000000 INFO @ Fri, 05 Jul 2019 23:58:01: 7000000 INFO @ Fri, 05 Jul 2019 23:58:03: 11000000 INFO @ Fri, 05 Jul 2019 23:58:05: 8000000 INFO @ Fri, 05 Jul 2019 23:58:09: 12000000 INFO @ Fri, 05 Jul 2019 23:58:10: 8000000 INFO @ Fri, 05 Jul 2019 23:58:13: 9000000 INFO @ Fri, 05 Jul 2019 23:58:15: 13000000 INFO @ Fri, 05 Jul 2019 23:58:19: 9000000 INFO @ Fri, 05 Jul 2019 23:58:21: 10000000 INFO @ Fri, 05 Jul 2019 23:58:21: 14000000 INFO @ Fri, 05 Jul 2019 23:58:27: 15000000 INFO @ Fri, 05 Jul 2019 23:58:28: 10000000 INFO @ Fri, 05 Jul 2019 23:58:29: 11000000 INFO @ Fri, 05 Jul 2019 23:58:33: 16000000 INFO @ Fri, 05 Jul 2019 23:58:36: 11000000 INFO @ Fri, 05 Jul 2019 23:58:37: 12000000 INFO @ Fri, 05 Jul 2019 23:58:39: 17000000 INFO @ Fri, 05 Jul 2019 23:58:45: 13000000 INFO @ Fri, 05 Jul 2019 23:58:45: 12000000 INFO @ Fri, 05 Jul 2019 23:58:45: 18000000 INFO @ Fri, 05 Jul 2019 23:58:52: 19000000 INFO @ Fri, 05 Jul 2019 23:58:53: 14000000 INFO @ Fri, 05 Jul 2019 23:58:54: 13000000 INFO @ Fri, 05 Jul 2019 23:58:58: 20000000 INFO @ Fri, 05 Jul 2019 23:59:00: 15000000 INFO @ Fri, 05 Jul 2019 23:59:02: 14000000 INFO @ Fri, 05 Jul 2019 23:59:03: 21000000 INFO @ Fri, 05 Jul 2019 23:59:08: 16000000 INFO @ Fri, 05 Jul 2019 23:59:09: 22000000 INFO @ Fri, 05 Jul 2019 23:59:11: 15000000 INFO @ Fri, 05 Jul 2019 23:59:16: 23000000 INFO @ Fri, 05 Jul 2019 23:59:16: 17000000 INFO @ Fri, 05 Jul 2019 23:59:20: 16000000 INFO @ Fri, 05 Jul 2019 23:59:22: 24000000 INFO @ Fri, 05 Jul 2019 23:59:24: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:59:29: 17000000 INFO @ Fri, 05 Jul 2019 23:59:29: 25000000 INFO @ Fri, 05 Jul 2019 23:59:32: 19000000 INFO @ Fri, 05 Jul 2019 23:59:34: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:59:34: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:59:34: #1 total tags in treatment: 12536516 INFO @ Fri, 05 Jul 2019 23:59:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:59:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:59:34: #1 tags after filtering in treatment: 5299855 INFO @ Fri, 05 Jul 2019 23:59:34: #1 Redundant rate of treatment: 0.58 INFO @ Fri, 05 Jul 2019 23:59:34: #1 finished! INFO @ Fri, 05 Jul 2019 23:59:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:59:34: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:59:34: 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 @ Fri, 05 Jul 2019 23:59:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:59:37: 18000000 INFO @ Fri, 05 Jul 2019 23:59:41: 20000000 INFO @ Fri, 05 Jul 2019 23:59:45: 19000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:59:49: 21000000 INFO @ Fri, 05 Jul 2019 23:59:53: 20000000 INFO @ Fri, 05 Jul 2019 23:59:57: 22000000 INFO @ Sat, 06 Jul 2019 00:00:01: 21000000 INFO @ Sat, 06 Jul 2019 00:00:06: 23000000 INFO @ Sat, 06 Jul 2019 00:00:08: 22000000 INFO @ Sat, 06 Jul 2019 00:00:14: 24000000 INFO @ Sat, 06 Jul 2019 00:00:16: 23000000 INFO @ Sat, 06 Jul 2019 00:00:22: 25000000 INFO @ Sat, 06 Jul 2019 00:00:25: 24000000 INFO @ Sat, 06 Jul 2019 00:00:28: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:00:28: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:00:28: #1 total tags in treatment: 12536516 INFO @ Sat, 06 Jul 2019 00:00:28: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:00:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:00:28: #1 tags after filtering in treatment: 5299855 INFO @ Sat, 06 Jul 2019 00:00:28: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 06 Jul 2019 00:00:28: #1 finished! INFO @ Sat, 06 Jul 2019 00:00:28: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:00:29: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:00:29: 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 @ Sat, 06 Jul 2019 00:00:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.20_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/SRX381275/SRX381275.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:00:33: 25000000 INFO @ Sat, 06 Jul 2019 00:00:38: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:00:38: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:00:38: #1 total tags in treatment: 12536516 INFO @ Sat, 06 Jul 2019 00:00:38: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:00:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:00:39: #1 tags after filtering in treatment: 5299855 INFO @ Sat, 06 Jul 2019 00:00:39: #1 Redundant rate of treatment: 0.58 INFO @ Sat, 06 Jul 2019 00:00:39: #1 finished! INFO @ Sat, 06 Jul 2019 00:00:39: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:00:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:00:39: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:00:39: 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 @ Sat, 06 Jul 2019 00:00:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.10_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/SRX381275/SRX381275.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381275/SRX381275.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling