Job ID = 2011681 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:15:26 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 ) 2019-07-05T17:15:27 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 ) 2019-07-05T17:15:27 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 ) 2019-07-05T17:15:27 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 ) 2019-07-05T17:27:51 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 ) 2019-07-05T17:27:51 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 ) 2019-07-05T17:31:53 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 ) 2019-07-05T17:32:32 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 ) 2019-07-05T17:33:59 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 ) 2019-07-05T17:34:45 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 ) 2019-07-05T17:34:45 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 ) 2019-07-05T17:44:14 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 : 24,399,739 reads read : 48,799,478 reads written : 48,799,478 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: 00:37:22 24399739 reads; of these: 24399739 (100.00%) were paired; of these: 4198195 (17.21%) aligned concordantly 0 times 16928441 (69.38%) aligned concordantly exactly 1 time 3273103 (13.41%) aligned concordantly >1 times ---- 4198195 pairs aligned concordantly 0 times; of these: 2032953 (48.42%) aligned discordantly 1 time ---- 2165242 pairs aligned 0 times concordantly or discordantly; of these: 4330484 mates make up the pairs; of these: 3115612 (71.95%) aligned 0 times 337797 (7.80%) aligned exactly 1 time 877075 (20.25%) aligned >1 times 93.62% overall alignment rate Time searching: 00:37:22 Overall time: 00:37:22 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 28 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] 1786093 / 22135596 = 0.0807 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 04:00:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.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 04:00:58: #1 read tag files... INFO @ Sat, 06 Jul 2019 04:00:58: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 04:00:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.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 04:00:59: #1 read tag files... INFO @ Sat, 06 Jul 2019 04:00:59: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 04:01:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.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 04:01:00: #1 read tag files... INFO @ Sat, 06 Jul 2019 04:01:00: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 04:01:17: 1000000 INFO @ Sat, 06 Jul 2019 04:01:19: 1000000 INFO @ Sat, 06 Jul 2019 04:01:20: 1000000 INFO @ Sat, 06 Jul 2019 04:01:36: 2000000 INFO @ Sat, 06 Jul 2019 04:01:40: 2000000 INFO @ Sat, 06 Jul 2019 04:01:41: 2000000 INFO @ Sat, 06 Jul 2019 04:01:54: 3000000 INFO @ Sat, 06 Jul 2019 04:02:01: 3000000 INFO @ Sat, 06 Jul 2019 04:02:02: 3000000 INFO @ Sat, 06 Jul 2019 04:02:13: 4000000 INFO @ Sat, 06 Jul 2019 04:02:22: 4000000 INFO @ Sat, 06 Jul 2019 04:02:22: 4000000 INFO @ Sat, 06 Jul 2019 04:02:32: 5000000 INFO @ Sat, 06 Jul 2019 04:02:43: 5000000 INFO @ Sat, 06 Jul 2019 04:02:43: 5000000 INFO @ Sat, 06 Jul 2019 04:02:51: 6000000 INFO @ Sat, 06 Jul 2019 04:03:04: 6000000 INFO @ Sat, 06 Jul 2019 04:03:04: 6000000 INFO @ Sat, 06 Jul 2019 04:03:10: 7000000 INFO @ Sat, 06 Jul 2019 04:03:25: 7000000 INFO @ Sat, 06 Jul 2019 04:03:26: 7000000 INFO @ Sat, 06 Jul 2019 04:03:28: 8000000 INFO @ Sat, 06 Jul 2019 04:03:46: 8000000 INFO @ Sat, 06 Jul 2019 04:03:46: 8000000 INFO @ Sat, 06 Jul 2019 04:03:47: 9000000 INFO @ Sat, 06 Jul 2019 04:04:05: 10000000 INFO @ Sat, 06 Jul 2019 04:04:06: 9000000 INFO @ Sat, 06 Jul 2019 04:04:07: 9000000 INFO @ Sat, 06 Jul 2019 04:04:23: 11000000 INFO @ Sat, 06 Jul 2019 04:04:27: 10000000 INFO @ Sat, 06 Jul 2019 04:04:27: 10000000 INFO @ Sat, 06 Jul 2019 04:04:42: 12000000 INFO @ Sat, 06 Jul 2019 04:04:47: 11000000 INFO @ Sat, 06 Jul 2019 04:04:48: 11000000 INFO @ Sat, 06 Jul 2019 04:05:00: 13000000 INFO @ Sat, 06 Jul 2019 04:05:08: 12000000 INFO @ Sat, 06 Jul 2019 04:05:08: 12000000 INFO @ Sat, 06 Jul 2019 04:05:19: 14000000 INFO @ Sat, 06 Jul 2019 04:05:28: 13000000 INFO @ Sat, 06 Jul 2019 04:05:29: 13000000 INFO @ Sat, 06 Jul 2019 04:05:37: 15000000 INFO @ Sat, 06 Jul 2019 04:05:48: 14000000 INFO @ Sat, 06 Jul 2019 04:05:49: 14000000 INFO @ Sat, 06 Jul 2019 04:05:55: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 04:06:09: 15000000 INFO @ Sat, 06 Jul 2019 04:06:09: 15000000 INFO @ Sat, 06 Jul 2019 04:06:14: 17000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 04:06:29: 16000000 INFO @ Sat, 06 Jul 2019 04:06:30: 16000000 INFO @ Sat, 06 Jul 2019 04:06:32: 18000000 INFO @ Sat, 06 Jul 2019 04:06:50: 17000000 INFO @ Sat, 06 Jul 2019 04:06:50: 17000000 INFO @ Sat, 06 Jul 2019 04:06:51: 19000000 INFO @ Sat, 06 Jul 2019 04:07:10: 20000000 INFO @ Sat, 06 Jul 2019 04:07:10: 18000000 INFO @ Sat, 06 Jul 2019 04:07:11: 18000000 INFO @ Sat, 06 Jul 2019 04:07:28: 21000000 INFO @ Sat, 06 Jul 2019 04:07:31: 19000000 INFO @ Sat, 06 Jul 2019 04:07:32: 19000000 INFO @ Sat, 06 Jul 2019 04:07:46: 22000000 INFO @ Sat, 06 Jul 2019 04:07:52: 20000000 INFO @ Sat, 06 Jul 2019 04:07:52: 20000000 INFO @ Sat, 06 Jul 2019 04:08:05: 23000000 INFO @ Sat, 06 Jul 2019 04:08:12: 21000000 INFO @ Sat, 06 Jul 2019 04:08:13: 21000000 INFO @ Sat, 06 Jul 2019 04:08:23: 24000000 INFO @ Sat, 06 Jul 2019 04:08:32: 22000000 INFO @ Sat, 06 Jul 2019 04:08:33: 22000000 INFO @ Sat, 06 Jul 2019 04:08:41: 25000000 INFO @ Sat, 06 Jul 2019 04:08:53: 23000000 INFO @ Sat, 06 Jul 2019 04:08:54: 23000000 INFO @ Sat, 06 Jul 2019 04:09:00: 26000000 INFO @ Sat, 06 Jul 2019 04:09:13: 24000000 INFO @ Sat, 06 Jul 2019 04:09:14: 24000000 INFO @ Sat, 06 Jul 2019 04:09:18: 27000000 INFO @ Sat, 06 Jul 2019 04:09:34: 25000000 INFO @ Sat, 06 Jul 2019 04:09:34: 25000000 INFO @ Sat, 06 Jul 2019 04:09:37: 28000000 INFO @ Sat, 06 Jul 2019 04:09:54: 26000000 INFO @ Sat, 06 Jul 2019 04:09:55: 26000000 INFO @ Sat, 06 Jul 2019 04:09:56: 29000000 INFO @ Sat, 06 Jul 2019 04:10:14: 30000000 INFO @ Sat, 06 Jul 2019 04:10:15: 27000000 INFO @ Sat, 06 Jul 2019 04:10:16: 27000000 INFO @ Sat, 06 Jul 2019 04:10:33: 31000000 INFO @ Sat, 06 Jul 2019 04:10:36: 28000000 INFO @ Sat, 06 Jul 2019 04:10:37: 28000000 INFO @ Sat, 06 Jul 2019 04:10:51: 32000000 INFO @ Sat, 06 Jul 2019 04:10:56: 29000000 INFO @ Sat, 06 Jul 2019 04:10:57: 29000000 INFO @ Sat, 06 Jul 2019 04:11:09: 33000000 INFO @ Sat, 06 Jul 2019 04:11:17: 30000000 INFO @ Sat, 06 Jul 2019 04:11:18: 30000000 INFO @ Sat, 06 Jul 2019 04:11:28: 34000000 INFO @ Sat, 06 Jul 2019 04:11:38: 31000000 INFO @ Sat, 06 Jul 2019 04:11:39: 31000000 INFO @ Sat, 06 Jul 2019 04:11:46: 35000000 INFO @ Sat, 06 Jul 2019 04:11:58: 32000000 INFO @ Sat, 06 Jul 2019 04:11:59: 32000000 INFO @ Sat, 06 Jul 2019 04:12:05: 36000000 INFO @ Sat, 06 Jul 2019 04:12:19: 33000000 INFO @ Sat, 06 Jul 2019 04:12:20: 33000000 INFO @ Sat, 06 Jul 2019 04:12:24: 37000000 INFO @ Sat, 06 Jul 2019 04:12:40: 34000000 INFO @ Sat, 06 Jul 2019 04:12:41: 34000000 INFO @ Sat, 06 Jul 2019 04:12:42: 38000000 INFO @ Sat, 06 Jul 2019 04:13:00: 39000000 INFO @ Sat, 06 Jul 2019 04:13:01: 35000000 INFO @ Sat, 06 Jul 2019 04:13:02: 35000000 INFO @ Sat, 06 Jul 2019 04:13:19: 40000000 INFO @ Sat, 06 Jul 2019 04:13:21: 36000000 INFO @ Sat, 06 Jul 2019 04:13:23: 36000000 INFO @ Sat, 06 Jul 2019 04:13:38: 41000000 INFO @ Sat, 06 Jul 2019 04:13:42: 37000000 INFO @ Sat, 06 Jul 2019 04:13:44: 37000000 INFO @ Sat, 06 Jul 2019 04:13:56: 42000000 INFO @ Sat, 06 Jul 2019 04:13:58: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 04:13:58: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 04:13:58: #1 total tags in treatment: 18501641 INFO @ Sat, 06 Jul 2019 04:13:58: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 04:13:58: #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 04:13:59: #1 tags after filtering in treatment: 11447574 INFO @ Sat, 06 Jul 2019 04:13:59: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 06 Jul 2019 04:13:59: #1 finished! INFO @ Sat, 06 Jul 2019 04:13:59: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 04:13:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 04:14:00: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 04:14:00: 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 04:14:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.05_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/SRX4560562/SRX4560562.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 04:14:03: 38000000 INFO @ Sat, 06 Jul 2019 04:14:04: 38000000 INFO @ Sat, 06 Jul 2019 04:14:22: 39000000 INFO @ Sat, 06 Jul 2019 04:14:23: 39000000 INFO @ Sat, 06 Jul 2019 04:14:41: 40000000 INFO @ Sat, 06 Jul 2019 04:14:42: 40000000 INFO @ Sat, 06 Jul 2019 04:14:59: 41000000 INFO @ Sat, 06 Jul 2019 04:15:00: 41000000 INFO @ Sat, 06 Jul 2019 04:15:18: 42000000 INFO @ Sat, 06 Jul 2019 04:15:19: 42000000 INFO @ Sat, 06 Jul 2019 04:15:20: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 04:15:20: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 04:15:20: #1 total tags in treatment: 18501641 INFO @ Sat, 06 Jul 2019 04:15:20: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 04:15:20: #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 04:15:20: #1 tags after filtering in treatment: 11447574 INFO @ Sat, 06 Jul 2019 04:15:20: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 06 Jul 2019 04:15:20: #1 finished! INFO @ Sat, 06 Jul 2019 04:15:20: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 04:15:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 04:15:21: #1 tag size is determined as 126 bps INFO @ Sat, 06 Jul 2019 04:15:21: #1 tag size = 126 INFO @ Sat, 06 Jul 2019 04:15:21: #1 total tags in treatment: 18501641 INFO @ Sat, 06 Jul 2019 04:15:21: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 04:15:21: #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 04:15:21: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 04:15:21: 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 04:15:21: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 04:15:21: #1 tags after filtering in treatment: 11447574 INFO @ Sat, 06 Jul 2019 04:15:21: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 06 Jul 2019 04:15:21: #1 finished! INFO @ Sat, 06 Jul 2019 04:15:21: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 04:15:21: #2 looking for paired plus/minus strand peaks... cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.10_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/SRX4560562/SRX4560562.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 04:15:22: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 04:15:22: 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 04:15:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.20_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/SRX4560562/SRX4560562.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4560562/SRX4560562.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling