Job ID = 5791480 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:31:06 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 ) 2020-04-22T00:43:56 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 ) 2020-04-22T00:43:56 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 ) 2020-04-22T00:43:56 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 ) spots read : 32,384,792 reads read : 64,769,584 reads written : 64,769,584 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: 00:08:21 32384792 reads; of these: 32384792 (100.00%) were paired; of these: 18357154 (56.68%) aligned concordantly 0 times 12456012 (38.46%) aligned concordantly exactly 1 time 1571626 (4.85%) aligned concordantly >1 times ---- 18357154 pairs aligned concordantly 0 times; of these: 25433 (0.14%) aligned discordantly 1 time ---- 18331721 pairs aligned 0 times concordantly or discordantly; of these: 36663442 mates make up the pairs; of these: 36466079 (99.46%) aligned 0 times 163955 (0.45%) aligned exactly 1 time 33408 (0.09%) aligned >1 times 43.70% overall alignment rate Time searching: 00:08:21 Overall time: 00:08:21 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] 3481758 / 14039475 = 0.2480 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 10:01:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.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 10:01:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:01:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:01:18: 1000000 INFO @ Wed, 22 Apr 2020 10:01:23: 2000000 INFO @ Wed, 22 Apr 2020 10:01:27: 3000000 INFO @ Wed, 22 Apr 2020 10:01:31: 4000000 INFO @ Wed, 22 Apr 2020 10:01:36: 5000000 INFO @ Wed, 22 Apr 2020 10:01:41: 6000000 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 10:01:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.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 10:01:44: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:01:44: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:01:46: 7000000 INFO @ Wed, 22 Apr 2020 10:01:48: 1000000 INFO @ Wed, 22 Apr 2020 10:01:51: 8000000 INFO @ Wed, 22 Apr 2020 10:01:53: 2000000 INFO @ Wed, 22 Apr 2020 10:01:56: 9000000 INFO @ Wed, 22 Apr 2020 10:01:58: 3000000 INFO @ Wed, 22 Apr 2020 10:02:01: 10000000 INFO @ Wed, 22 Apr 2020 10:02:03: 4000000 INFO @ Wed, 22 Apr 2020 10:02:06: 11000000 INFO @ Wed, 22 Apr 2020 10:02:08: 5000000 INFO @ Wed, 22 Apr 2020 10:02:11: 12000000 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 10:02:13: 6000000 INFO @ Wed, 22 Apr 2020 10:02:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.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 10:02:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:02:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:02:16: 13000000 INFO @ Wed, 22 Apr 2020 10:02:17: 7000000 INFO @ Wed, 22 Apr 2020 10:02:19: 1000000 INFO @ Wed, 22 Apr 2020 10:02:21: 14000000 INFO @ Wed, 22 Apr 2020 10:02:22: 8000000 INFO @ Wed, 22 Apr 2020 10:02:25: 2000000 INFO @ Wed, 22 Apr 2020 10:02:26: 15000000 INFO @ Wed, 22 Apr 2020 10:02:27: 9000000 INFO @ Wed, 22 Apr 2020 10:02:30: 3000000 INFO @ Wed, 22 Apr 2020 10:02:31: 16000000 INFO @ Wed, 22 Apr 2020 10:02:32: 10000000 INFO @ Wed, 22 Apr 2020 10:02:35: 17000000 INFO @ Wed, 22 Apr 2020 10:02:36: 4000000 INFO @ Wed, 22 Apr 2020 10:02:37: 11000000 INFO @ Wed, 22 Apr 2020 10:02:40: 18000000 INFO @ Wed, 22 Apr 2020 10:02:42: 5000000 INFO @ Wed, 22 Apr 2020 10:02:42: 12000000 INFO @ Wed, 22 Apr 2020 10:02:45: 19000000 INFO @ Wed, 22 Apr 2020 10:02:47: 13000000 INFO @ Wed, 22 Apr 2020 10:02:47: 6000000 INFO @ Wed, 22 Apr 2020 10:02:50: 20000000 INFO @ Wed, 22 Apr 2020 10:02:52: 14000000 INFO @ Wed, 22 Apr 2020 10:02:53: 7000000 INFO @ Wed, 22 Apr 2020 10:02:55: 21000000 INFO @ Wed, 22 Apr 2020 10:02:57: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:02:57: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:02:57: #1 total tags in treatment: 10549638 INFO @ Wed, 22 Apr 2020 10:02:57: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:02:57: #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 10:02:57: #1 tags after filtering in treatment: 7957474 INFO @ Wed, 22 Apr 2020 10:02:57: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 22 Apr 2020 10:02:57: #1 finished! INFO @ Wed, 22 Apr 2020 10:02:57: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:02:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:02:57: 15000000 INFO @ Wed, 22 Apr 2020 10:02:57: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:02:57: 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 @ Wed, 22 Apr 2020 10:02:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.05_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/SRX7409571/SRX7409571.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:02:59: 8000000 INFO @ Wed, 22 Apr 2020 10:03:02: 16000000 INFO @ Wed, 22 Apr 2020 10:03:06: 9000000 INFO @ Wed, 22 Apr 2020 10:03:07: 17000000 INFO @ Wed, 22 Apr 2020 10:03:12: 18000000 INFO @ Wed, 22 Apr 2020 10:03:12: 10000000 INFO @ Wed, 22 Apr 2020 10:03:17: 19000000 INFO @ Wed, 22 Apr 2020 10:03:18: 11000000 INFO @ Wed, 22 Apr 2020 10:03:22: 20000000 INFO @ Wed, 22 Apr 2020 10:03:23: 12000000 INFO @ Wed, 22 Apr 2020 10:03:27: 21000000 INFO @ Wed, 22 Apr 2020 10:03:27: 13000000 INFO @ Wed, 22 Apr 2020 10:03:28: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:03:28: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:03:28: #1 total tags in treatment: 10549638 INFO @ Wed, 22 Apr 2020 10:03:28: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:03:28: #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 10:03:28: #1 tags after filtering in treatment: 7957474 INFO @ Wed, 22 Apr 2020 10:03:28: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 22 Apr 2020 10:03:28: #1 finished! INFO @ Wed, 22 Apr 2020 10:03:28: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:03:29: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:03:29: 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 10:03:29: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.10_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/SRX7409571/SRX7409571.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:03:33: 14000000 INFO @ Wed, 22 Apr 2020 10:03:39: 15000000 INFO @ Wed, 22 Apr 2020 10:03:44: 16000000 INFO @ Wed, 22 Apr 2020 10:03:49: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:03:53: 18000000 INFO @ Wed, 22 Apr 2020 10:04:01: 19000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:04:08: 20000000 INFO @ Wed, 22 Apr 2020 10:04:14: 21000000 INFO @ Wed, 22 Apr 2020 10:04:17: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:04:17: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:04:17: #1 total tags in treatment: 10549638 INFO @ Wed, 22 Apr 2020 10:04:17: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:04:17: #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 10:04:17: #1 tags after filtering in treatment: 7957474 INFO @ Wed, 22 Apr 2020 10:04:17: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 22 Apr 2020 10:04:17: #1 finished! INFO @ Wed, 22 Apr 2020 10:04:17: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:04:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:04:17: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:04:17: 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 @ Wed, 22 Apr 2020 10:04:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.20_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/SRX7409571/SRX7409571.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409571/SRX7409571.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling