Job ID = 5791112 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:32:08 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 ) 2020-04-21T23:36:48 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 ) 2020-04-21T23:38:21 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 ) 2020-04-21T23:43:55 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 ) 2020-04-21T23:43:55 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 : 23,675,473 reads read : 47,350,946 reads written : 47,350,946 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: 00:10:35 23675473 reads; of these: 23675473 (100.00%) were paired; of these: 2537093 (10.72%) aligned concordantly 0 times 18808446 (79.44%) aligned concordantly exactly 1 time 2329934 (9.84%) aligned concordantly >1 times ---- 2537093 pairs aligned concordantly 0 times; of these: 307428 (12.12%) aligned discordantly 1 time ---- 2229665 pairs aligned 0 times concordantly or discordantly; of these: 4459330 mates make up the pairs; of these: 3707352 (83.14%) aligned 0 times 455631 (10.22%) aligned exactly 1 time 296347 (6.65%) aligned >1 times 92.17% overall alignment rate Time searching: 00:10:35 Overall time: 00:10:35 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] 768965 / 21428274 = 0.0359 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 09:12:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.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 09:12:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:12:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:12:12: 1000000 INFO @ Wed, 22 Apr 2020 09:12:17: 2000000 INFO @ Wed, 22 Apr 2020 09:12:22: 3000000 INFO @ Wed, 22 Apr 2020 09:12:27: 4000000 INFO @ Wed, 22 Apr 2020 09:12:32: 5000000 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 09:12:37: 6000000 INFO @ Wed, 22 Apr 2020 09:12:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.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 09:12:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:12:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:12:42: 7000000 INFO @ Wed, 22 Apr 2020 09:12:42: 1000000 INFO @ Wed, 22 Apr 2020 09:12:47: 8000000 INFO @ Wed, 22 Apr 2020 09:12:47: 2000000 INFO @ Wed, 22 Apr 2020 09:12:52: 9000000 INFO @ Wed, 22 Apr 2020 09:12:52: 3000000 INFO @ Wed, 22 Apr 2020 09:12:57: 4000000 INFO @ Wed, 22 Apr 2020 09:12:57: 10000000 INFO @ Wed, 22 Apr 2020 09:13:02: 5000000 INFO @ Wed, 22 Apr 2020 09:13:02: 11000000 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 09:13:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.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 09:13:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:13:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:13:08: 6000000 INFO @ Wed, 22 Apr 2020 09:13:08: 12000000 INFO @ Wed, 22 Apr 2020 09:13:13: 1000000 INFO @ Wed, 22 Apr 2020 09:13:13: 7000000 INFO @ Wed, 22 Apr 2020 09:13:14: 13000000 INFO @ Wed, 22 Apr 2020 09:13:18: 2000000 INFO @ Wed, 22 Apr 2020 09:13:19: 8000000 INFO @ Wed, 22 Apr 2020 09:13:19: 14000000 INFO @ Wed, 22 Apr 2020 09:13:24: 3000000 INFO @ Wed, 22 Apr 2020 09:13:25: 9000000 INFO @ Wed, 22 Apr 2020 09:13:25: 15000000 INFO @ Wed, 22 Apr 2020 09:13:29: 4000000 INFO @ Wed, 22 Apr 2020 09:13:31: 10000000 INFO @ Wed, 22 Apr 2020 09:13:31: 16000000 INFO @ Wed, 22 Apr 2020 09:13:35: 5000000 INFO @ Wed, 22 Apr 2020 09:13:37: 11000000 INFO @ Wed, 22 Apr 2020 09:13:37: 17000000 INFO @ Wed, 22 Apr 2020 09:13:40: 6000000 INFO @ Wed, 22 Apr 2020 09:13:43: 12000000 INFO @ Wed, 22 Apr 2020 09:13:43: 18000000 INFO @ Wed, 22 Apr 2020 09:13:45: 7000000 INFO @ Wed, 22 Apr 2020 09:13:48: 19000000 INFO @ Wed, 22 Apr 2020 09:13:48: 13000000 INFO @ Wed, 22 Apr 2020 09:13:51: 8000000 INFO @ Wed, 22 Apr 2020 09:13:53: 20000000 INFO @ Wed, 22 Apr 2020 09:13:54: 14000000 INFO @ Wed, 22 Apr 2020 09:13:56: 9000000 INFO @ Wed, 22 Apr 2020 09:13:59: 21000000 INFO @ Wed, 22 Apr 2020 09:13:59: 15000000 INFO @ Wed, 22 Apr 2020 09:14:02: 10000000 INFO @ Wed, 22 Apr 2020 09:14:04: 22000000 INFO @ Wed, 22 Apr 2020 09:14:04: 16000000 INFO @ Wed, 22 Apr 2020 09:14:07: 11000000 INFO @ Wed, 22 Apr 2020 09:14:09: 23000000 INFO @ Wed, 22 Apr 2020 09:14:10: 17000000 INFO @ Wed, 22 Apr 2020 09:14:12: 12000000 INFO @ Wed, 22 Apr 2020 09:14:14: 24000000 INFO @ Wed, 22 Apr 2020 09:14:15: 18000000 INFO @ Wed, 22 Apr 2020 09:14:18: 13000000 INFO @ Wed, 22 Apr 2020 09:14:19: 25000000 INFO @ Wed, 22 Apr 2020 09:14:20: 19000000 INFO @ Wed, 22 Apr 2020 09:14:23: 14000000 INFO @ Wed, 22 Apr 2020 09:14:25: 26000000 INFO @ Wed, 22 Apr 2020 09:14:25: 20000000 INFO @ Wed, 22 Apr 2020 09:14:28: 15000000 INFO @ Wed, 22 Apr 2020 09:14:30: 27000000 INFO @ Wed, 22 Apr 2020 09:14:31: 21000000 INFO @ Wed, 22 Apr 2020 09:14:34: 16000000 INFO @ Wed, 22 Apr 2020 09:14:35: 28000000 INFO @ Wed, 22 Apr 2020 09:14:36: 22000000 INFO @ Wed, 22 Apr 2020 09:14:39: 17000000 INFO @ Wed, 22 Apr 2020 09:14:40: 29000000 INFO @ Wed, 22 Apr 2020 09:14:41: 23000000 INFO @ Wed, 22 Apr 2020 09:14:44: 18000000 INFO @ Wed, 22 Apr 2020 09:14:45: 30000000 INFO @ Wed, 22 Apr 2020 09:14:46: 24000000 INFO @ Wed, 22 Apr 2020 09:14:49: 19000000 INFO @ Wed, 22 Apr 2020 09:14:50: 31000000 INFO @ Wed, 22 Apr 2020 09:14:51: 25000000 INFO @ Wed, 22 Apr 2020 09:14:55: 20000000 INFO @ Wed, 22 Apr 2020 09:14:56: 32000000 INFO @ Wed, 22 Apr 2020 09:14:57: 26000000 INFO @ Wed, 22 Apr 2020 09:15:00: 21000000 INFO @ Wed, 22 Apr 2020 09:15:01: 33000000 INFO @ Wed, 22 Apr 2020 09:15:02: 27000000 INFO @ Wed, 22 Apr 2020 09:15:05: 22000000 INFO @ Wed, 22 Apr 2020 09:15:06: 34000000 INFO @ Wed, 22 Apr 2020 09:15:07: 28000000 INFO @ Wed, 22 Apr 2020 09:15:11: 23000000 INFO @ Wed, 22 Apr 2020 09:15:11: 35000000 INFO @ Wed, 22 Apr 2020 09:15:12: 29000000 INFO @ Wed, 22 Apr 2020 09:15:16: 24000000 INFO @ Wed, 22 Apr 2020 09:15:17: 36000000 INFO @ Wed, 22 Apr 2020 09:15:18: 30000000 INFO @ Wed, 22 Apr 2020 09:15:21: 25000000 INFO @ Wed, 22 Apr 2020 09:15:22: 37000000 INFO @ Wed, 22 Apr 2020 09:15:23: 31000000 INFO @ Wed, 22 Apr 2020 09:15:27: 26000000 INFO @ Wed, 22 Apr 2020 09:15:27: 38000000 INFO @ Wed, 22 Apr 2020 09:15:28: 32000000 INFO @ Wed, 22 Apr 2020 09:15:32: 27000000 INFO @ Wed, 22 Apr 2020 09:15:33: 39000000 INFO @ Wed, 22 Apr 2020 09:15:33: 33000000 INFO @ Wed, 22 Apr 2020 09:15:37: 28000000 INFO @ Wed, 22 Apr 2020 09:15:38: 40000000 INFO @ Wed, 22 Apr 2020 09:15:39: 34000000 INFO @ Wed, 22 Apr 2020 09:15:43: 29000000 INFO @ Wed, 22 Apr 2020 09:15:43: 41000000 INFO @ Wed, 22 Apr 2020 09:15:44: 35000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:15:48: 30000000 INFO @ Wed, 22 Apr 2020 09:15:49: 42000000 INFO @ Wed, 22 Apr 2020 09:15:49: 36000000 INFO @ Wed, 22 Apr 2020 09:15:49: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 09:15:49: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 09:15:49: #1 total tags in treatment: 20371448 INFO @ Wed, 22 Apr 2020 09:15:49: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:15:49: #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 09:15:50: #1 tags after filtering in treatment: 12002557 INFO @ Wed, 22 Apr 2020 09:15:50: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 22 Apr 2020 09:15:50: #1 finished! INFO @ Wed, 22 Apr 2020 09:15:50: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:15:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:15:50: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 09:15:50: 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 09:15:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.05_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/SRX6078423/SRX6078423.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:15:53: 31000000 INFO @ Wed, 22 Apr 2020 09:15:54: 37000000 INFO @ Wed, 22 Apr 2020 09:15:58: 32000000 INFO @ Wed, 22 Apr 2020 09:15:59: 38000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:16:04: 33000000 INFO @ Wed, 22 Apr 2020 09:16:05: 39000000 INFO @ Wed, 22 Apr 2020 09:16:09: 34000000 INFO @ Wed, 22 Apr 2020 09:16:09: 40000000 INFO @ Wed, 22 Apr 2020 09:16:14: 35000000 INFO @ Wed, 22 Apr 2020 09:16:15: 41000000 INFO @ Wed, 22 Apr 2020 09:16:19: 36000000 INFO @ Wed, 22 Apr 2020 09:16:19: 42000000 INFO @ Wed, 22 Apr 2020 09:16:20: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 09:16:20: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 09:16:20: #1 total tags in treatment: 20371448 INFO @ Wed, 22 Apr 2020 09:16:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:16:20: #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 09:16:21: #1 tags after filtering in treatment: 12002557 INFO @ Wed, 22 Apr 2020 09:16:21: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 22 Apr 2020 09:16:21: #1 finished! INFO @ Wed, 22 Apr 2020 09:16:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:16:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:16:21: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 09:16:21: 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 09:16:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.10_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/SRX6078423/SRX6078423.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:16:24: 37000000 INFO @ Wed, 22 Apr 2020 09:16:29: 38000000 INFO @ Wed, 22 Apr 2020 09:16:34: 39000000 INFO @ Wed, 22 Apr 2020 09:16:39: 40000000 INFO @ Wed, 22 Apr 2020 09:16:44: 41000000 INFO @ Wed, 22 Apr 2020 09:16:49: 42000000 INFO @ Wed, 22 Apr 2020 09:16:50: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 09:16:50: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 09:16:50: #1 total tags in treatment: 20371448 INFO @ Wed, 22 Apr 2020 09:16:50: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:16:50: #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 09:16:50: #1 tags after filtering in treatment: 12002557 INFO @ Wed, 22 Apr 2020 09:16:50: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 22 Apr 2020 09:16:50: #1 finished! INFO @ Wed, 22 Apr 2020 09:16:50: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:16:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:16:51: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 09:16:51: 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 09:16:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.20_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/SRX6078423/SRX6078423.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6078423/SRX6078423.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling