Job ID = 2010738 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T15:10:44 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 ) 2019-07-05T15:10:45 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 ) 2019-07-05T15:10:45 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 ) 2019-07-05T15:12:20 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 8,605,161 reads read : 17,210,322 reads written : 17,210,322 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: 00:08:09 8605161 reads; of these: 8605161 (100.00%) were paired; of these: 1577755 (18.33%) aligned concordantly 0 times 6235915 (72.47%) aligned concordantly exactly 1 time 791491 (9.20%) aligned concordantly >1 times ---- 1577755 pairs aligned concordantly 0 times; of these: 118932 (7.54%) aligned discordantly 1 time ---- 1458823 pairs aligned 0 times concordantly or discordantly; of these: 2917646 mates make up the pairs; of these: 2517100 (86.27%) aligned 0 times 308182 (10.56%) aligned exactly 1 time 92364 (3.17%) aligned >1 times 85.37% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:09 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 8 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] 88777 / 7121881 = 0.0125 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 @ Sat, 06 Jul 2019 00:38:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.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 @ Sat, 06 Jul 2019 00:38:59: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:38:59: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:39:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.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 @ Sat, 06 Jul 2019 00:39:00: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:39:00: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:39:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.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 @ Sat, 06 Jul 2019 00:39:01: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:39:01: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:39:10: 1000000 INFO @ Sat, 06 Jul 2019 00:39:10: 1000000 INFO @ Sat, 06 Jul 2019 00:39:12: 1000000 INFO @ Sat, 06 Jul 2019 00:39:19: 2000000 INFO @ Sat, 06 Jul 2019 00:39:21: 2000000 INFO @ Sat, 06 Jul 2019 00:39:24: 2000000 INFO @ Sat, 06 Jul 2019 00:39:28: 3000000 INFO @ Sat, 06 Jul 2019 00:39:32: 3000000 INFO @ Sat, 06 Jul 2019 00:39:35: 3000000 INFO @ Sat, 06 Jul 2019 00:39:37: 4000000 INFO @ Sat, 06 Jul 2019 00:39:44: 4000000 INFO @ Sat, 06 Jul 2019 00:39:46: 4000000 INFO @ Sat, 06 Jul 2019 00:39:46: 5000000 INFO @ Sat, 06 Jul 2019 00:39:55: 5000000 INFO @ Sat, 06 Jul 2019 00:39:56: 6000000 INFO @ Sat, 06 Jul 2019 00:39:57: 5000000 INFO @ Sat, 06 Jul 2019 00:40:05: 7000000 INFO @ Sat, 06 Jul 2019 00:40:06: 6000000 INFO @ Sat, 06 Jul 2019 00:40:09: 6000000 INFO @ Sat, 06 Jul 2019 00:40:14: 8000000 INFO @ Sat, 06 Jul 2019 00:40:17: 7000000 INFO @ Sat, 06 Jul 2019 00:40:20: 7000000 INFO @ Sat, 06 Jul 2019 00:40:23: 9000000 INFO @ Sat, 06 Jul 2019 00:40:28: 8000000 INFO @ Sat, 06 Jul 2019 00:40:31: 8000000 INFO @ Sat, 06 Jul 2019 00:40:32: 10000000 INFO @ Sat, 06 Jul 2019 00:40:40: 9000000 INFO @ Sat, 06 Jul 2019 00:40:42: 11000000 INFO @ Sat, 06 Jul 2019 00:40:42: 9000000 INFO @ Sat, 06 Jul 2019 00:40:51: 10000000 INFO @ Sat, 06 Jul 2019 00:40:51: 12000000 INFO @ Sat, 06 Jul 2019 00:40:53: 10000000 INFO @ Sat, 06 Jul 2019 00:41:00: 13000000 INFO @ Sat, 06 Jul 2019 00:41:02: 11000000 INFO @ Sat, 06 Jul 2019 00:41:05: 11000000 INFO @ Sat, 06 Jul 2019 00:41:09: 14000000 INFO @ Sat, 06 Jul 2019 00:41:13: 12000000 INFO @ Sat, 06 Jul 2019 00:41:14: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:41:14: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:41:14: #1 total tags in treatment: 6939464 INFO @ Sat, 06 Jul 2019 00:41:14: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:41:14: #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 00:41:14: #1 tags after filtering in treatment: 5563618 INFO @ Sat, 06 Jul 2019 00:41:14: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 06 Jul 2019 00:41:14: #1 finished! INFO @ Sat, 06 Jul 2019 00:41:14: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:41:14: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:41:15: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:41:15: 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 00:41:15: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:41:16: 12000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.10_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/SRX386919/SRX386919.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:41:23: 13000000 INFO @ Sat, 06 Jul 2019 00:41:25: 13000000 INFO @ Sat, 06 Jul 2019 00:41:32: 14000000 INFO @ Sat, 06 Jul 2019 00:41:34: 14000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:41:36: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:41:36: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:41:36: #1 total tags in treatment: 6939464 INFO @ Sat, 06 Jul 2019 00:41:36: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:41:36: #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 00:41:36: #1 tags after filtering in treatment: 5563618 INFO @ Sat, 06 Jul 2019 00:41:36: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 06 Jul 2019 00:41:36: #1 finished! INFO @ Sat, 06 Jul 2019 00:41:36: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:41:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:41:37: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:41:37: 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 00:41:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.05_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/SRX386919/SRX386919.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:41:38: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:41:38: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:41:38: #1 total tags in treatment: 6939464 INFO @ Sat, 06 Jul 2019 00:41:38: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:41:38: #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 00:41:38: #1 tags after filtering in treatment: 5563618 INFO @ Sat, 06 Jul 2019 00:41:38: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 06 Jul 2019 00:41:38: #1 finished! INFO @ Sat, 06 Jul 2019 00:41:38: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:41:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:41:39: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 00:41:39: 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 00:41:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.20_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/SRX386919/SRX386919.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX386919/SRX386919.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling