Job ID = 2011737 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T17:16:44 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 ) 2019-07-05T17:17:05 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 ) 2019-07-05T17:17:05 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 : 8,511,459 reads read : 17,022,918 reads written : 17,022,918 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: 00:05:37 8511459 reads; of these: 8511459 (100.00%) were paired; of these: 1273886 (14.97%) aligned concordantly 0 times 6110848 (71.80%) aligned concordantly exactly 1 time 1126725 (13.24%) aligned concordantly >1 times ---- 1273886 pairs aligned concordantly 0 times; of these: 181469 (14.25%) aligned discordantly 1 time ---- 1092417 pairs aligned 0 times concordantly or discordantly; of these: 2184834 mates make up the pairs; of these: 1939753 (88.78%) aligned 0 times 126868 (5.81%) aligned exactly 1 time 118213 (5.41%) aligned >1 times 88.61% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 415754 / 7417207 = 0.0561 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 02:31:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.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 02:31:30: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:31:30: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:31:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.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 02:31:31: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:31:31: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:31:37: 1000000 INFO @ Sat, 06 Jul 2019 02:31:37: 1000000 INFO @ Sat, 06 Jul 2019 02:31:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.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 02:31:40: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:31:40: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:31:44: 2000000 INFO @ Sat, 06 Jul 2019 02:31:45: 2000000 INFO @ Sat, 06 Jul 2019 02:31:47: 1000000 INFO @ Sat, 06 Jul 2019 02:31:50: 3000000 INFO @ Sat, 06 Jul 2019 02:31:52: 3000000 INFO @ Sat, 06 Jul 2019 02:31:53: 2000000 INFO @ Sat, 06 Jul 2019 02:31:57: 4000000 INFO @ Sat, 06 Jul 2019 02:31:58: 3000000 INFO @ Sat, 06 Jul 2019 02:32:00: 4000000 INFO @ Sat, 06 Jul 2019 02:32:03: 5000000 INFO @ Sat, 06 Jul 2019 02:32:04: 4000000 INFO @ Sat, 06 Jul 2019 02:32:08: 5000000 INFO @ Sat, 06 Jul 2019 02:32:09: 6000000 INFO @ Sat, 06 Jul 2019 02:32:10: 5000000 INFO @ Sat, 06 Jul 2019 02:32:15: 6000000 INFO @ Sat, 06 Jul 2019 02:32:16: 6000000 INFO @ Sat, 06 Jul 2019 02:32:16: 7000000 INFO @ Sat, 06 Jul 2019 02:32:22: 7000000 INFO @ Sat, 06 Jul 2019 02:32:22: 8000000 INFO @ Sat, 06 Jul 2019 02:32:23: 7000000 INFO @ Sat, 06 Jul 2019 02:32:27: 8000000 INFO @ Sat, 06 Jul 2019 02:32:28: 9000000 INFO @ Sat, 06 Jul 2019 02:32:30: 8000000 INFO @ Sat, 06 Jul 2019 02:32:33: 9000000 INFO @ Sat, 06 Jul 2019 02:32:35: 10000000 INFO @ Sat, 06 Jul 2019 02:32:38: 9000000 INFO @ Sat, 06 Jul 2019 02:32:39: 10000000 INFO @ Sat, 06 Jul 2019 02:32:41: 11000000 INFO @ Sat, 06 Jul 2019 02:32:44: 11000000 INFO @ Sat, 06 Jul 2019 02:32:45: 10000000 INFO @ Sat, 06 Jul 2019 02:32:47: 12000000 INFO @ Sat, 06 Jul 2019 02:32:50: 12000000 INFO @ Sat, 06 Jul 2019 02:32:53: 11000000 INFO @ Sat, 06 Jul 2019 02:32:54: 13000000 INFO @ Sat, 06 Jul 2019 02:32:56: 13000000 INFO @ Sat, 06 Jul 2019 02:33:00: 14000000 INFO @ Sat, 06 Jul 2019 02:33:00: 12000000 INFO @ Sat, 06 Jul 2019 02:33:02: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:33:02: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:33:02: #1 total tags in treatment: 6827728 INFO @ Sat, 06 Jul 2019 02:33:02: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:33:02: #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 02:33:02: 14000000 INFO @ Sat, 06 Jul 2019 02:33:02: #1 tags after filtering in treatment: 5099054 INFO @ Sat, 06 Jul 2019 02:33:02: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 02:33:02: #1 finished! INFO @ Sat, 06 Jul 2019 02:33:02: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:33:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:33:02: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:33:02: 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 02:33:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.10_peaks.narrowPeak: No such file or directory INFO @ Sat, 06 Jul 2019 02:33:03: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:33:03: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:33:03: #1 total tags in treatment: 6827728 INFO @ Sat, 06 Jul 2019 02:33:03: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:33:03: #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 02:33:03: #1 tags after filtering in treatment: 5099054 INFO @ Sat, 06 Jul 2019 02:33:03: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 02:33:03: #1 finished! INFO @ Sat, 06 Jul 2019 02:33:03: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:33:03: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:33:04: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:33:04: 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, 06 Jul 2019 02:33:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.20_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/SRX4915176/SRX4915176.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:33:08: 13000000 INFO @ Sat, 06 Jul 2019 02:33:15: 14000000 INFO @ Sat, 06 Jul 2019 02:33:17: #1 tag size is determined as 42 bps INFO @ Sat, 06 Jul 2019 02:33:17: #1 tag size = 42 INFO @ Sat, 06 Jul 2019 02:33:17: #1 total tags in treatment: 6827728 INFO @ Sat, 06 Jul 2019 02:33:17: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:33:17: #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 02:33:17: #1 tags after filtering in treatment: 5099054 INFO @ Sat, 06 Jul 2019 02:33:17: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 06 Jul 2019 02:33:17: #1 finished! INFO @ Sat, 06 Jul 2019 02:33:17: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:33:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:33:17: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:33:17: 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 02:33:17: Process for pairing-model is terminated! BedGraph に変換しました。 cut: /home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.05_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4915176/SRX4915176.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。