Job ID = 2640987 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-08-24T11:13:26 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 ) 2019-08-24T11:13:43 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 ) 2019-08-24T11:14:48 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 ) 2019-08-24T11:14:48 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 ) 2019-08-24T11:19:09 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 ) 2019-08-24T11:21:33 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 : 12,504,382 reads read : 25,008,764 reads written : 25,008,764 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: 00:16:09 12504382 reads; of these: 12504382 (100.00%) were paired; of these: 334658 (2.68%) aligned concordantly 0 times 10696909 (85.55%) aligned concordantly exactly 1 time 1472815 (11.78%) aligned concordantly >1 times ---- 334658 pairs aligned concordantly 0 times; of these: 89958 (26.88%) aligned discordantly 1 time ---- 244700 pairs aligned 0 times concordantly or discordantly; of these: 489400 mates make up the pairs; of these: 435809 (89.05%) aligned 0 times 23570 (4.82%) aligned exactly 1 time 30021 (6.13%) aligned >1 times 98.26% overall alignment rate Time searching: 00:16:09 Overall time: 00:16:09 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 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] 148719 / 12256972 = 0.0121 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:00:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.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, 24 Aug 2019 21:00:06: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:00:06: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:00:16: 1000000 INFO @ Sat, 24 Aug 2019 21:00:25: 2000000 INFO @ Sat, 24 Aug 2019 21:00:34: 3000000 INFO @ Sat, 24 Aug 2019 21:00:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.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, 24 Aug 2019 21:00:36: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:00:36: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:00:44: 4000000 INFO @ Sat, 24 Aug 2019 21:00:51: 1000000 INFO @ Sat, 24 Aug 2019 21:00:55: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:01:05: 6000000 INFO @ Sat, 24 Aug 2019 21:01:06: 2000000 INFO @ Sat, 24 Aug 2019 21:01:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.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, 24 Aug 2019 21:01:06: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:01:06: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:01:15: 7000000 INFO @ Sat, 24 Aug 2019 21:01:18: 1000000 INFO @ Sat, 24 Aug 2019 21:01:21: 3000000 INFO @ Sat, 24 Aug 2019 21:01:25: 8000000 INFO @ Sat, 24 Aug 2019 21:01:30: 2000000 INFO @ Sat, 24 Aug 2019 21:01:35: 9000000 INFO @ Sat, 24 Aug 2019 21:01:36: 4000000 INFO @ Sat, 24 Aug 2019 21:01:42: 3000000 INFO @ Sat, 24 Aug 2019 21:01:44: 10000000 INFO @ Sat, 24 Aug 2019 21:01:51: 5000000 INFO @ Sat, 24 Aug 2019 21:01:53: 4000000 INFO @ Sat, 24 Aug 2019 21:01:54: 11000000 INFO @ Sat, 24 Aug 2019 21:02:04: 12000000 INFO @ Sat, 24 Aug 2019 21:02:05: 5000000 INFO @ Sat, 24 Aug 2019 21:02:06: 6000000 INFO @ Sat, 24 Aug 2019 21:02:14: 13000000 INFO @ Sat, 24 Aug 2019 21:02:16: 6000000 INFO @ Sat, 24 Aug 2019 21:02:21: 7000000 INFO @ Sat, 24 Aug 2019 21:02:24: 14000000 INFO @ Sat, 24 Aug 2019 21:02:28: 7000000 INFO @ Sat, 24 Aug 2019 21:02:34: 15000000 INFO @ Sat, 24 Aug 2019 21:02:36: 8000000 INFO @ Sat, 24 Aug 2019 21:02:39: 8000000 INFO @ Sat, 24 Aug 2019 21:02:44: 16000000 INFO @ Sat, 24 Aug 2019 21:02:51: 9000000 INFO @ Sat, 24 Aug 2019 21:02:52: 9000000 INFO @ Sat, 24 Aug 2019 21:02:54: 17000000 INFO @ Sat, 24 Aug 2019 21:03:04: 18000000 INFO @ Sat, 24 Aug 2019 21:03:04: 10000000 INFO @ Sat, 24 Aug 2019 21:03:07: 10000000 INFO @ Sat, 24 Aug 2019 21:03:14: 19000000 INFO @ Sat, 24 Aug 2019 21:03:16: 11000000 INFO @ Sat, 24 Aug 2019 21:03:22: 11000000 INFO @ Sat, 24 Aug 2019 21:03:24: 20000000 INFO @ Sat, 24 Aug 2019 21:03:29: 12000000 INFO @ Sat, 24 Aug 2019 21:03:34: 21000000 INFO @ Sat, 24 Aug 2019 21:03:37: 12000000 INFO @ Sat, 24 Aug 2019 21:03:41: 13000000 INFO @ Sat, 24 Aug 2019 21:03:45: 22000000 INFO @ Sat, 24 Aug 2019 21:03:53: 13000000 INFO @ Sat, 24 Aug 2019 21:03:54: 14000000 INFO @ Sat, 24 Aug 2019 21:03:56: 23000000 INFO @ Sat, 24 Aug 2019 21:04:07: 15000000 INFO @ Sat, 24 Aug 2019 21:04:08: 24000000 INFO @ Sat, 24 Aug 2019 21:04:09: 14000000 INFO @ Sat, 24 Aug 2019 21:04:11: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:04:11: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:04:11: #1 total tags in treatment: 12021468 INFO @ Sat, 24 Aug 2019 21:04:11: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:04:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:04:11: #1 tags after filtering in treatment: 8932248 INFO @ Sat, 24 Aug 2019 21:04:11: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 24 Aug 2019 21:04:11: #1 finished! INFO @ Sat, 24 Aug 2019 21:04:11: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:04:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:04:12: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:04:12: 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, 24 Aug 2019 21:04:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.05_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/SRX4936093/SRX4936093.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:04:19: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:04:25: 15000000 INFO @ Sat, 24 Aug 2019 21:04:32: 17000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:04:41: 16000000 INFO @ Sat, 24 Aug 2019 21:04:44: 18000000 INFO @ Sat, 24 Aug 2019 21:04:56: 17000000 INFO @ Sat, 24 Aug 2019 21:04:57: 19000000 INFO @ Sat, 24 Aug 2019 21:05:10: 20000000 INFO @ Sat, 24 Aug 2019 21:05:11: 18000000 INFO @ Sat, 24 Aug 2019 21:05:22: 21000000 INFO @ Sat, 24 Aug 2019 21:05:25: 19000000 INFO @ Sat, 24 Aug 2019 21:05:35: 22000000 INFO @ Sat, 24 Aug 2019 21:05:40: 20000000 INFO @ Sat, 24 Aug 2019 21:05:47: 23000000 INFO @ Sat, 24 Aug 2019 21:05:55: 21000000 INFO @ Sat, 24 Aug 2019 21:06:00: 24000000 INFO @ Sat, 24 Aug 2019 21:06:03: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:06:03: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:06:03: #1 total tags in treatment: 12021468 INFO @ Sat, 24 Aug 2019 21:06:03: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:06:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:06:03: #1 tags after filtering in treatment: 8932248 INFO @ Sat, 24 Aug 2019 21:06:03: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 24 Aug 2019 21:06:03: #1 finished! INFO @ Sat, 24 Aug 2019 21:06:03: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:06:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:06:04: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:06:04: 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, 24 Aug 2019 21:06:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.20_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/SRX4936093/SRX4936093.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:06:09: 22000000 INFO @ Sat, 24 Aug 2019 21:06:23: 23000000 INFO @ Sat, 24 Aug 2019 21:06:37: 24000000 INFO @ Sat, 24 Aug 2019 21:06:40: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:06:40: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:06:40: #1 total tags in treatment: 12021468 INFO @ Sat, 24 Aug 2019 21:06:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:06:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:06:41: #1 tags after filtering in treatment: 8932248 INFO @ Sat, 24 Aug 2019 21:06:41: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 24 Aug 2019 21:06:41: #1 finished! INFO @ Sat, 24 Aug 2019 21:06:41: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:06:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:06:41: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:06:41: 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, 24 Aug 2019 21:06:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.10_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/SRX4936093/SRX4936093.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936093/SRX4936093.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling