Job ID = 2011837 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:54:52 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 ) 2019-07-05T17:54:52 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 : 24,981,880 reads read : 49,963,760 reads written : 49,963,760 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 Warning: skipping mate #1 of read 'SRR8313285.4544650 4544650 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313285.4544650 4544650 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313285.6940477 6940477 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313285.6940477 6940477 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313285.7404105 7404105 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313285.7404105 7404105 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313285.16250719 16250719 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313285.16250719 16250719 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313285.18045629 18045629 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313285.18045629 18045629 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313285.19954611 19954611 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313285.19954611 19954611 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313285.21729867 21729867 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313285.21729867 21729867 length=1' because it was < 2 characters long Multiseed full-index search: 00:26:13 24981880 reads; of these: 24981880 (100.00%) were paired; of these: 953325 (3.82%) aligned concordantly 0 times 17139824 (68.61%) aligned concordantly exactly 1 time 6888731 (27.57%) aligned concordantly >1 times ---- 953325 pairs aligned concordantly 0 times; of these: 47046 (4.93%) aligned discordantly 1 time ---- 906279 pairs aligned 0 times concordantly or discordantly; of these: 1812558 mates make up the pairs; of these: 1289583 (71.15%) aligned 0 times 331743 (18.30%) aligned exactly 1 time 191232 (10.55%) aligned >1 times 97.42% overall alignment rate Time searching: 00:26:13 Overall time: 00:26:13 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 20 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] 6125468 / 24040385 = 0.2548 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 03:56:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.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 03:56:14: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:56:14: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:56:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.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 03:56:15: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:56:15: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:56:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.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 03:56:16: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:56:16: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:56:22: 1000000 INFO @ Sat, 06 Jul 2019 03:56:24: 1000000 INFO @ Sat, 06 Jul 2019 03:56:27: 1000000 INFO @ Sat, 06 Jul 2019 03:56:30: 2000000 INFO @ Sat, 06 Jul 2019 03:56:33: 2000000 INFO @ Sat, 06 Jul 2019 03:56:38: 3000000 INFO @ Sat, 06 Jul 2019 03:56:38: 2000000 INFO @ Sat, 06 Jul 2019 03:56:42: 3000000 INFO @ Sat, 06 Jul 2019 03:56:45: 4000000 INFO @ Sat, 06 Jul 2019 03:56:49: 3000000 INFO @ Sat, 06 Jul 2019 03:56:50: 4000000 INFO @ Sat, 06 Jul 2019 03:56:53: 5000000 INFO @ Sat, 06 Jul 2019 03:56:59: 5000000 INFO @ Sat, 06 Jul 2019 03:57:00: 4000000 INFO @ Sat, 06 Jul 2019 03:57:01: 6000000 INFO @ Sat, 06 Jul 2019 03:57:08: 6000000 INFO @ Sat, 06 Jul 2019 03:57:09: 7000000 INFO @ Sat, 06 Jul 2019 03:57:11: 5000000 INFO @ Sat, 06 Jul 2019 03:57:16: 8000000 INFO @ Sat, 06 Jul 2019 03:57:17: 7000000 INFO @ Sat, 06 Jul 2019 03:57:22: 6000000 INFO @ Sat, 06 Jul 2019 03:57:24: 9000000 INFO @ Sat, 06 Jul 2019 03:57:26: 8000000 INFO @ Sat, 06 Jul 2019 03:57:32: 10000000 INFO @ Sat, 06 Jul 2019 03:57:33: 7000000 INFO @ Sat, 06 Jul 2019 03:57:34: 9000000 INFO @ Sat, 06 Jul 2019 03:57:40: 11000000 INFO @ Sat, 06 Jul 2019 03:57:43: 10000000 INFO @ Sat, 06 Jul 2019 03:57:44: 8000000 INFO @ Sat, 06 Jul 2019 03:57:47: 12000000 INFO @ Sat, 06 Jul 2019 03:57:52: 11000000 INFO @ Sat, 06 Jul 2019 03:57:55: 9000000 INFO @ Sat, 06 Jul 2019 03:57:55: 13000000 INFO @ Sat, 06 Jul 2019 03:58:01: 12000000 INFO @ Sat, 06 Jul 2019 03:58:03: 14000000 INFO @ Sat, 06 Jul 2019 03:58:05: 10000000 INFO @ Sat, 06 Jul 2019 03:58:09: 13000000 INFO @ Sat, 06 Jul 2019 03:58:10: 15000000 INFO @ Sat, 06 Jul 2019 03:58:16: 11000000 INFO @ Sat, 06 Jul 2019 03:58:18: 14000000 INFO @ Sat, 06 Jul 2019 03:58:18: 16000000 INFO @ Sat, 06 Jul 2019 03:58:26: 17000000 INFO @ Sat, 06 Jul 2019 03:58:27: 15000000 INFO @ Sat, 06 Jul 2019 03:58:27: 12000000 INFO @ Sat, 06 Jul 2019 03:58:34: 18000000 INFO @ Sat, 06 Jul 2019 03:58:35: 16000000 INFO @ Sat, 06 Jul 2019 03:58:38: 13000000 INFO @ Sat, 06 Jul 2019 03:58:41: 19000000 INFO @ Sat, 06 Jul 2019 03:58:44: 17000000 INFO @ Sat, 06 Jul 2019 03:58:49: 14000000 INFO @ Sat, 06 Jul 2019 03:58:49: 20000000 INFO @ Sat, 06 Jul 2019 03:58:53: 18000000 INFO @ Sat, 06 Jul 2019 03:58:57: 21000000 INFO @ Sat, 06 Jul 2019 03:58:59: 15000000 INFO @ Sat, 06 Jul 2019 03:59:02: 19000000 INFO @ Sat, 06 Jul 2019 03:59:04: 22000000 INFO @ Sat, 06 Jul 2019 03:59:10: 16000000 INFO @ Sat, 06 Jul 2019 03:59:10: 20000000 INFO @ Sat, 06 Jul 2019 03:59:11: 23000000 INFO @ Sat, 06 Jul 2019 03:59:19: 24000000 INFO @ Sat, 06 Jul 2019 03:59:19: 21000000 INFO @ Sat, 06 Jul 2019 03:59:21: 17000000 INFO @ Sat, 06 Jul 2019 03:59:26: 25000000 INFO @ Sat, 06 Jul 2019 03:59:27: 22000000 INFO @ Sat, 06 Jul 2019 03:59:32: 18000000 INFO @ Sat, 06 Jul 2019 03:59:34: 26000000 INFO @ Sat, 06 Jul 2019 03:59:35: 23000000 INFO @ Sat, 06 Jul 2019 03:59:41: 27000000 INFO @ Sat, 06 Jul 2019 03:59:42: 19000000 INFO @ Sat, 06 Jul 2019 03:59:44: 24000000 INFO @ Sat, 06 Jul 2019 03:59:48: 28000000 INFO @ Sat, 06 Jul 2019 03:59:52: 25000000 INFO @ Sat, 06 Jul 2019 03:59:53: 20000000 INFO @ Sat, 06 Jul 2019 03:59:56: 29000000 INFO @ Sat, 06 Jul 2019 04:00:00: 26000000 INFO @ Sat, 06 Jul 2019 04:00:03: 30000000 INFO @ Sat, 06 Jul 2019 04:00:04: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 04:00:08: 27000000 INFO @ Sat, 06 Jul 2019 04:00:11: 31000000 INFO @ Sat, 06 Jul 2019 04:00:14: 22000000 INFO @ Sat, 06 Jul 2019 04:00:17: 28000000 INFO @ Sat, 06 Jul 2019 04:00:18: 32000000 INFO @ Sat, 06 Jul 2019 04:00:24: 23000000 INFO @ Sat, 06 Jul 2019 04:00:25: 29000000 INFO @ Sat, 06 Jul 2019 04:00:26: 33000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 04:00:33: 34000000 INFO @ Sat, 06 Jul 2019 04:00:33: 30000000 INFO @ Sat, 06 Jul 2019 04:00:35: 24000000 INFO @ Sat, 06 Jul 2019 04:00:41: 35000000 INFO @ Sat, 06 Jul 2019 04:00:42: 31000000 INFO @ Sat, 06 Jul 2019 04:00:45: 25000000 INFO @ Sat, 06 Jul 2019 04:00:48: 36000000 INFO @ Sat, 06 Jul 2019 04:00:50: 32000000 INFO @ Sat, 06 Jul 2019 04:00:51: #1 tag size is determined as 74 bps INFO @ Sat, 06 Jul 2019 04:00:51: #1 tag size = 74 INFO @ Sat, 06 Jul 2019 04:00:51: #1 total tags in treatment: 17904024 INFO @ Sat, 06 Jul 2019 04:00:51: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 04:00:51: #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 04:00:52: #1 tags after filtering in treatment: 9824739 INFO @ Sat, 06 Jul 2019 04:00:52: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 06 Jul 2019 04:00:52: #1 finished! INFO @ Sat, 06 Jul 2019 04:00:52: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 04:00:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 04:00:53: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 04:00:53: 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 04:00:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.05_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/SRX5126593/SRX5126593.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 04:00:55: 26000000 INFO @ Sat, 06 Jul 2019 04:00:58: 33000000 INFO @ Sat, 06 Jul 2019 04:01:05: 27000000 INFO @ Sat, 06 Jul 2019 04:01:06: 34000000 INFO @ Sat, 06 Jul 2019 04:01:14: 35000000 INFO @ Sat, 06 Jul 2019 04:01:15: 28000000 INFO @ Sat, 06 Jul 2019 04:01:23: 36000000 INFO @ Sat, 06 Jul 2019 04:01:25: 29000000 INFO @ Sat, 06 Jul 2019 04:01:27: #1 tag size is determined as 74 bps INFO @ Sat, 06 Jul 2019 04:01:27: #1 tag size = 74 INFO @ Sat, 06 Jul 2019 04:01:27: #1 total tags in treatment: 17904024 INFO @ Sat, 06 Jul 2019 04:01:27: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 04:01:27: #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 04:01:27: #1 tags after filtering in treatment: 9824739 INFO @ Sat, 06 Jul 2019 04:01:27: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 06 Jul 2019 04:01:27: #1 finished! INFO @ Sat, 06 Jul 2019 04:01:27: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 04:01:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 04:01:28: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 04:01:28: 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 04:01:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.10_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/SRX5126593/SRX5126593.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 04:01:35: 30000000 INFO @ Sat, 06 Jul 2019 04:01:45: 31000000 INFO @ Sat, 06 Jul 2019 04:01:54: 32000000 INFO @ Sat, 06 Jul 2019 04:02:04: 33000000 INFO @ Sat, 06 Jul 2019 04:02:14: 34000000 INFO @ Sat, 06 Jul 2019 04:02:24: 35000000 INFO @ Sat, 06 Jul 2019 04:02:33: 36000000 INFO @ Sat, 06 Jul 2019 04:02:38: #1 tag size is determined as 74 bps INFO @ Sat, 06 Jul 2019 04:02:38: #1 tag size = 74 INFO @ Sat, 06 Jul 2019 04:02:38: #1 total tags in treatment: 17904024 INFO @ Sat, 06 Jul 2019 04:02:38: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 04:02:38: #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 04:02:38: #1 tags after filtering in treatment: 9824739 INFO @ Sat, 06 Jul 2019 04:02:38: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 06 Jul 2019 04:02:38: #1 finished! INFO @ Sat, 06 Jul 2019 04:02:38: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 04:02:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 04:02:39: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 04:02:39: 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 04:02:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 8 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126593/SRX5126593.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling