Job ID = 2011832 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:48:52 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 ) 2019-07-05T17:48:52 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 ) 2019-07-05T17:48:52 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 ) 2019-07-05T17:52:02 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 ) 2019-07-05T17:54:16 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 : 14,258,450 reads read : 28,516,900 reads written : 28,516,900 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 'SRR8313282.432752 432752 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313282.432752 432752 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313282.1485272 1485272 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313282.1485272 1485272 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313282.3590787 3590787 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313282.3590787 3590787 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313282.3641831 3641831 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313282.3641831 3641831 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313282.4023564 4023564 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313282.4023564 4023564 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR8313282.11554149 11554149 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR8313282.11554149 11554149 length=1' because it was < 2 characters long Multiseed full-index search: 00:15:07 14258450 reads; of these: 14258450 (100.00%) were paired; of these: 563608 (3.95%) aligned concordantly 0 times 11362556 (79.69%) aligned concordantly exactly 1 time 2332286 (16.36%) aligned concordantly >1 times ---- 563608 pairs aligned concordantly 0 times; of these: 45715 (8.11%) aligned discordantly 1 time ---- 517893 pairs aligned 0 times concordantly or discordantly; of these: 1035786 mates make up the pairs; of these: 803147 (77.54%) aligned 0 times 154939 (14.96%) aligned exactly 1 time 77700 (7.50%) aligned >1 times 97.18% overall alignment rate Time searching: 00:15:07 Overall time: 00:15:07 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] 2030518 / 13736489 = 0.1478 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 03:29:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.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 03:29:37: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:29:37: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:29:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.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 03:29:37: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:29:37: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:29:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.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 03:29:38: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:29:38: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:29:47: 1000000 INFO @ Sat, 06 Jul 2019 03:29:51: 1000000 INFO @ Sat, 06 Jul 2019 03:29:51: 1000000 INFO @ Sat, 06 Jul 2019 03:29:56: 2000000 INFO @ Sat, 06 Jul 2019 03:30:04: 2000000 INFO @ Sat, 06 Jul 2019 03:30:05: 2000000 INFO @ Sat, 06 Jul 2019 03:30:06: 3000000 INFO @ Sat, 06 Jul 2019 03:30:16: 4000000 INFO @ Sat, 06 Jul 2019 03:30:18: 3000000 INFO @ Sat, 06 Jul 2019 03:30:19: 3000000 INFO @ Sat, 06 Jul 2019 03:30:25: 5000000 INFO @ Sat, 06 Jul 2019 03:30:32: 4000000 INFO @ Sat, 06 Jul 2019 03:30:33: 4000000 INFO @ Sat, 06 Jul 2019 03:30:35: 6000000 INFO @ Sat, 06 Jul 2019 03:30:45: 7000000 INFO @ Sat, 06 Jul 2019 03:30:46: 5000000 INFO @ Sat, 06 Jul 2019 03:30:46: 5000000 INFO @ Sat, 06 Jul 2019 03:30:54: 8000000 INFO @ Sat, 06 Jul 2019 03:31:00: 6000000 INFO @ Sat, 06 Jul 2019 03:31:00: 6000000 INFO @ Sat, 06 Jul 2019 03:31:04: 9000000 INFO @ Sat, 06 Jul 2019 03:31:13: 7000000 INFO @ Sat, 06 Jul 2019 03:31:14: 10000000 INFO @ Sat, 06 Jul 2019 03:31:14: 7000000 INFO @ Sat, 06 Jul 2019 03:31:23: 11000000 INFO @ Sat, 06 Jul 2019 03:31:27: 8000000 INFO @ Sat, 06 Jul 2019 03:31:28: 8000000 INFO @ Sat, 06 Jul 2019 03:31:33: 12000000 INFO @ Sat, 06 Jul 2019 03:31:41: 9000000 INFO @ Sat, 06 Jul 2019 03:31:42: 9000000 INFO @ Sat, 06 Jul 2019 03:31:43: 13000000 INFO @ Sat, 06 Jul 2019 03:31:52: 14000000 INFO @ Sat, 06 Jul 2019 03:31:54: 10000000 INFO @ Sat, 06 Jul 2019 03:31:55: 10000000 INFO @ Sat, 06 Jul 2019 03:32:02: 15000000 INFO @ Sat, 06 Jul 2019 03:32:08: 11000000 INFO @ Sat, 06 Jul 2019 03:32:09: 11000000 INFO @ Sat, 06 Jul 2019 03:32:11: 16000000 INFO @ Sat, 06 Jul 2019 03:32:21: 17000000 INFO @ Sat, 06 Jul 2019 03:32:22: 12000000 INFO @ Sat, 06 Jul 2019 03:32:22: 12000000 INFO @ Sat, 06 Jul 2019 03:32:31: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:32:35: 13000000 INFO @ Sat, 06 Jul 2019 03:32:36: 13000000 INFO @ Sat, 06 Jul 2019 03:32:41: 19000000 INFO @ Sat, 06 Jul 2019 03:32:49: 14000000 INFO @ Sat, 06 Jul 2019 03:32:49: 14000000 INFO @ Sat, 06 Jul 2019 03:32:50: 20000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:32:59: 21000000 INFO @ Sat, 06 Jul 2019 03:33:02: 15000000 INFO @ Sat, 06 Jul 2019 03:33:03: 15000000 INFO @ Sat, 06 Jul 2019 03:33:09: 22000000 INFO @ Sat, 06 Jul 2019 03:33:15: 16000000 INFO @ Sat, 06 Jul 2019 03:33:16: 16000000 INFO @ Sat, 06 Jul 2019 03:33:18: 23000000 INFO @ Sat, 06 Jul 2019 03:33:24: #1 tag size is determined as 73 bps INFO @ Sat, 06 Jul 2019 03:33:24: #1 tag size = 73 INFO @ Sat, 06 Jul 2019 03:33:24: #1 total tags in treatment: 11667644 INFO @ Sat, 06 Jul 2019 03:33:24: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:33:24: #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 03:33:25: #1 tags after filtering in treatment: 7553002 INFO @ Sat, 06 Jul 2019 03:33:25: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 06 Jul 2019 03:33:25: #1 finished! INFO @ Sat, 06 Jul 2019 03:33:25: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:33:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:33:25: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:33:25: 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 03:33:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.05_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/SRX5126590/SRX5126590.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:33:29: 17000000 INFO @ Sat, 06 Jul 2019 03:33:29: 17000000 INFO @ Sat, 06 Jul 2019 03:33:42: 18000000 INFO @ Sat, 06 Jul 2019 03:33:43: 18000000 INFO @ Sat, 06 Jul 2019 03:33:55: 19000000 INFO @ Sat, 06 Jul 2019 03:33:56: 19000000 INFO @ Sat, 06 Jul 2019 03:34:08: 20000000 INFO @ Sat, 06 Jul 2019 03:34:09: 20000000 INFO @ Sat, 06 Jul 2019 03:34:21: 21000000 INFO @ Sat, 06 Jul 2019 03:34:22: 21000000 INFO @ Sat, 06 Jul 2019 03:34:34: 22000000 INFO @ Sat, 06 Jul 2019 03:34:35: 22000000 INFO @ Sat, 06 Jul 2019 03:34:48: 23000000 INFO @ Sat, 06 Jul 2019 03:34:49: 23000000 INFO @ Sat, 06 Jul 2019 03:34:56: #1 tag size is determined as 73 bps INFO @ Sat, 06 Jul 2019 03:34:56: #1 tag size = 73 INFO @ Sat, 06 Jul 2019 03:34:56: #1 total tags in treatment: 11667644 INFO @ Sat, 06 Jul 2019 03:34:56: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:34:56: #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 03:34:56: #1 tags after filtering in treatment: 7553002 INFO @ Sat, 06 Jul 2019 03:34:56: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 06 Jul 2019 03:34:56: #1 finished! INFO @ Sat, 06 Jul 2019 03:34:56: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:34:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:34:57: #1 tag size is determined as 73 bps INFO @ Sat, 06 Jul 2019 03:34:57: #1 tag size = 73 INFO @ Sat, 06 Jul 2019 03:34:57: #1 total tags in treatment: 11667644 INFO @ Sat, 06 Jul 2019 03:34:57: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:34:57: #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 03:34:57: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:34:57: 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 03:34:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.10_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/SRX5126590/SRX5126590.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:34:57: #1 tags after filtering in treatment: 7553002 INFO @ Sat, 06 Jul 2019 03:34:57: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 06 Jul 2019 03:34:57: #1 finished! INFO @ Sat, 06 Jul 2019 03:34:57: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:34:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:34:58: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 03:34:58: 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 03:34:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.20_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/SRX5126590/SRX5126590.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5126590/SRX5126590.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling