Job ID = 5791638 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:49:03 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 ) 2020-04-22T00:49:03 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 ) 2020-04-22T00:52:06 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 ) 2020-04-22T00:52:56 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 ) 2020-04-22T00:52:56 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 ) 2020-04-22T01:01:38 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 : 25,129,827 reads read : 50,259,654 reads written : 50,259,654 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: 00:12:55 25129827 reads; of these: 25129827 (100.00%) were paired; of these: 812328 (3.23%) aligned concordantly 0 times 22147880 (88.13%) aligned concordantly exactly 1 time 2169619 (8.63%) aligned concordantly >1 times ---- 812328 pairs aligned concordantly 0 times; of these: 24899 (3.07%) aligned discordantly 1 time ---- 787429 pairs aligned 0 times concordantly or discordantly; of these: 1574858 mates make up the pairs; of these: 1259699 (79.99%) aligned 0 times 278355 (17.67%) aligned exactly 1 time 36804 (2.34%) aligned >1 times 97.49% overall alignment rate Time searching: 00:12:56 Overall time: 00:12:56 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] 5111273 / 24326996 = 0.2101 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:27:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.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 @ Wed, 22 Apr 2020 10:27:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:27:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:27:44: 1000000 INFO @ Wed, 22 Apr 2020 10:27:49: 2000000 INFO @ Wed, 22 Apr 2020 10:27:55: 3000000 INFO @ Wed, 22 Apr 2020 10:28:00: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:28:05: 5000000 INFO @ Wed, 22 Apr 2020 10:28:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.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 @ Wed, 22 Apr 2020 10:28:06: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:28:06: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:28:11: 6000000 INFO @ Wed, 22 Apr 2020 10:28:12: 1000000 INFO @ Wed, 22 Apr 2020 10:28:17: 7000000 INFO @ Wed, 22 Apr 2020 10:28:18: 2000000 INFO @ Wed, 22 Apr 2020 10:28:23: 8000000 INFO @ Wed, 22 Apr 2020 10:28:24: 3000000 INFO @ Wed, 22 Apr 2020 10:28:29: 9000000 INFO @ Wed, 22 Apr 2020 10:28:30: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:28:35: 10000000 INFO @ Wed, 22 Apr 2020 10:28:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.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 @ Wed, 22 Apr 2020 10:28:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:28:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:28:36: 5000000 INFO @ Wed, 22 Apr 2020 10:28:42: 11000000 INFO @ Wed, 22 Apr 2020 10:28:43: 1000000 INFO @ Wed, 22 Apr 2020 10:28:43: 6000000 INFO @ Wed, 22 Apr 2020 10:28:49: 12000000 INFO @ Wed, 22 Apr 2020 10:28:50: 7000000 INFO @ Wed, 22 Apr 2020 10:28:51: 2000000 INFO @ Wed, 22 Apr 2020 10:28:55: 13000000 INFO @ Wed, 22 Apr 2020 10:28:56: 8000000 INFO @ Wed, 22 Apr 2020 10:29:00: 3000000 INFO @ Wed, 22 Apr 2020 10:29:02: 14000000 INFO @ Wed, 22 Apr 2020 10:29:03: 9000000 INFO @ Wed, 22 Apr 2020 10:29:08: 4000000 INFO @ Wed, 22 Apr 2020 10:29:09: 15000000 INFO @ Wed, 22 Apr 2020 10:29:10: 10000000 INFO @ Wed, 22 Apr 2020 10:29:15: 5000000 INFO @ Wed, 22 Apr 2020 10:29:15: 16000000 INFO @ Wed, 22 Apr 2020 10:29:17: 11000000 INFO @ Wed, 22 Apr 2020 10:29:22: 17000000 INFO @ Wed, 22 Apr 2020 10:29:23: 6000000 INFO @ Wed, 22 Apr 2020 10:29:23: 12000000 INFO @ Wed, 22 Apr 2020 10:29:29: 18000000 INFO @ Wed, 22 Apr 2020 10:29:30: 7000000 INFO @ Wed, 22 Apr 2020 10:29:30: 13000000 INFO @ Wed, 22 Apr 2020 10:29:36: 19000000 INFO @ Wed, 22 Apr 2020 10:29:37: 8000000 INFO @ Wed, 22 Apr 2020 10:29:37: 14000000 INFO @ Wed, 22 Apr 2020 10:29:42: 20000000 INFO @ Wed, 22 Apr 2020 10:29:44: 15000000 INFO @ Wed, 22 Apr 2020 10:29:44: 9000000 INFO @ Wed, 22 Apr 2020 10:29:49: 21000000 INFO @ Wed, 22 Apr 2020 10:29:50: 16000000 INFO @ Wed, 22 Apr 2020 10:29:51: 10000000 INFO @ Wed, 22 Apr 2020 10:29:56: 22000000 INFO @ Wed, 22 Apr 2020 10:29:57: 17000000 INFO @ Wed, 22 Apr 2020 10:29:58: 11000000 INFO @ Wed, 22 Apr 2020 10:30:03: 23000000 INFO @ Wed, 22 Apr 2020 10:30:04: 18000000 INFO @ Wed, 22 Apr 2020 10:30:05: 12000000 INFO @ Wed, 22 Apr 2020 10:30:09: 24000000 INFO @ Wed, 22 Apr 2020 10:30:10: 19000000 INFO @ Wed, 22 Apr 2020 10:30:12: 13000000 INFO @ Wed, 22 Apr 2020 10:30:16: 25000000 INFO @ Wed, 22 Apr 2020 10:30:17: 20000000 INFO @ Wed, 22 Apr 2020 10:30:19: 14000000 INFO @ Wed, 22 Apr 2020 10:30:23: 26000000 INFO @ Wed, 22 Apr 2020 10:30:24: 21000000 INFO @ Wed, 22 Apr 2020 10:30:27: 15000000 INFO @ Wed, 22 Apr 2020 10:30:30: 27000000 INFO @ Wed, 22 Apr 2020 10:30:31: 22000000 INFO @ Wed, 22 Apr 2020 10:30:34: 16000000 INFO @ Wed, 22 Apr 2020 10:30:36: 28000000 INFO @ Wed, 22 Apr 2020 10:30:37: 23000000 INFO @ Wed, 22 Apr 2020 10:30:41: 17000000 INFO @ Wed, 22 Apr 2020 10:30:43: 29000000 INFO @ Wed, 22 Apr 2020 10:30:44: 24000000 INFO @ Wed, 22 Apr 2020 10:30:48: 18000000 INFO @ Wed, 22 Apr 2020 10:30:50: 30000000 INFO @ Wed, 22 Apr 2020 10:30:51: 25000000 INFO @ Wed, 22 Apr 2020 10:30:55: 19000000 INFO @ Wed, 22 Apr 2020 10:30:56: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:30:57: 26000000 INFO @ Wed, 22 Apr 2020 10:31:02: 20000000 INFO @ Wed, 22 Apr 2020 10:31:03: 32000000 INFO @ Wed, 22 Apr 2020 10:31:04: 27000000 INFO @ Wed, 22 Apr 2020 10:31:09: 21000000 INFO @ Wed, 22 Apr 2020 10:31:10: 33000000 INFO @ Wed, 22 Apr 2020 10:31:11: 28000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:31:16: 22000000 INFO @ Wed, 22 Apr 2020 10:31:16: 34000000 INFO @ Wed, 22 Apr 2020 10:31:18: 29000000 INFO @ Wed, 22 Apr 2020 10:31:23: 35000000 INFO @ Wed, 22 Apr 2020 10:31:23: 23000000 INFO @ Wed, 22 Apr 2020 10:31:24: 30000000 INFO @ Wed, 22 Apr 2020 10:31:30: 36000000 INFO @ Wed, 22 Apr 2020 10:31:30: 24000000 INFO @ Wed, 22 Apr 2020 10:31:31: 31000000 INFO @ Wed, 22 Apr 2020 10:31:37: 37000000 INFO @ Wed, 22 Apr 2020 10:31:38: 25000000 INFO @ Wed, 22 Apr 2020 10:31:38: 32000000 INFO @ Wed, 22 Apr 2020 10:31:43: 38000000 INFO @ Wed, 22 Apr 2020 10:31:44: 33000000 INFO @ Wed, 22 Apr 2020 10:31:45: 26000000 INFO @ Wed, 22 Apr 2020 10:31:48: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:31:48: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:31:48: #1 total tags in treatment: 19207927 INFO @ Wed, 22 Apr 2020 10:31:48: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:31:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:31:49: #1 tags after filtering in treatment: 10840165 INFO @ Wed, 22 Apr 2020 10:31:49: #1 Redundant rate of treatment: 0.44 INFO @ Wed, 22 Apr 2020 10:31:49: #1 finished! INFO @ Wed, 22 Apr 2020 10:31:49: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:31:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:31:49: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:31:49: 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 @ Wed, 22 Apr 2020 10:31:49: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:31:51: 34000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.05_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/SRX7409604/SRX7409604.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:31:52: 27000000 INFO @ Wed, 22 Apr 2020 10:31:58: 35000000 INFO @ Wed, 22 Apr 2020 10:31:59: 28000000 INFO @ Wed, 22 Apr 2020 10:32:04: 36000000 INFO @ Wed, 22 Apr 2020 10:32:06: 29000000 INFO @ Wed, 22 Apr 2020 10:32:11: 37000000 INFO @ Wed, 22 Apr 2020 10:32:14: 30000000 INFO @ Wed, 22 Apr 2020 10:32:18: 38000000 INFO @ Wed, 22 Apr 2020 10:32:21: 31000000 INFO @ Wed, 22 Apr 2020 10:32:23: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:32:23: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:32:23: #1 total tags in treatment: 19207927 INFO @ Wed, 22 Apr 2020 10:32:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:32:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:32:23: #1 tags after filtering in treatment: 10840165 INFO @ Wed, 22 Apr 2020 10:32:23: #1 Redundant rate of treatment: 0.44 INFO @ Wed, 22 Apr 2020 10:32:23: #1 finished! INFO @ Wed, 22 Apr 2020 10:32:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:32:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:32:24: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:32:24: 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 @ Wed, 22 Apr 2020 10:32:24: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:32:28: 32000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.10_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/SRX7409604/SRX7409604.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:32:34: 33000000 INFO @ Wed, 22 Apr 2020 10:32:41: 34000000 INFO @ Wed, 22 Apr 2020 10:32:48: 35000000 INFO @ Wed, 22 Apr 2020 10:32:54: 36000000 INFO @ Wed, 22 Apr 2020 10:33:01: 37000000 INFO @ Wed, 22 Apr 2020 10:33:07: 38000000 INFO @ Wed, 22 Apr 2020 10:33:13: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:33:13: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:33:13: #1 total tags in treatment: 19207927 INFO @ Wed, 22 Apr 2020 10:33:13: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:33:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:33:13: #1 tags after filtering in treatment: 10840165 INFO @ Wed, 22 Apr 2020 10:33:13: #1 Redundant rate of treatment: 0.44 INFO @ Wed, 22 Apr 2020 10:33:13: #1 finished! INFO @ Wed, 22 Apr 2020 10:33:13: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:33:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:33:14: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:33:14: 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 @ Wed, 22 Apr 2020 10:33:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409604/SRX7409604.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling