Job ID = 5791300 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:26:35 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 ) 2020-04-22T00:26:35 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 ) 2020-04-22T00:29:40 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 ) 2020-04-22T00:32:13 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 ) 2020-04-22T00:32:29 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 ) 2020-04-22T00:35:25 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 ) 2020-04-22T00:35:25 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 ) 2020-04-22T00:35:25 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 : 24,396,910 reads read : 48,793,820 reads written : 48,793,820 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: 00:12:23 24396910 reads; of these: 24396910 (100.00%) were paired; of these: 565875 (2.32%) aligned concordantly 0 times 20968879 (85.95%) aligned concordantly exactly 1 time 2862156 (11.73%) aligned concordantly >1 times ---- 565875 pairs aligned concordantly 0 times; of these: 38604 (6.82%) aligned discordantly 1 time ---- 527271 pairs aligned 0 times concordantly or discordantly; of these: 1054542 mates make up the pairs; of these: 763377 (72.39%) aligned 0 times 238850 (22.65%) aligned exactly 1 time 52315 (4.96%) aligned >1 times 98.44% overall alignment rate Time searching: 00:12:23 Overall time: 00:12:23 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] 5630335 / 23839353 = 0.2362 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 09:59:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.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 09:59:30: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:59:30: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:59:34: 1000000 INFO @ Wed, 22 Apr 2020 09:59:38: 2000000 INFO @ Wed, 22 Apr 2020 09:59:42: 3000000 INFO @ Wed, 22 Apr 2020 09:59:47: 4000000 INFO @ Wed, 22 Apr 2020 09:59:51: 5000000 INFO @ Wed, 22 Apr 2020 09:59:55: 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 09:59:59: 7000000 INFO @ Wed, 22 Apr 2020 10:00:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.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 10:00:00: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:00:00: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:00:04: 8000000 INFO @ Wed, 22 Apr 2020 10:00:04: 1000000 INFO @ Wed, 22 Apr 2020 10:00:08: 9000000 INFO @ Wed, 22 Apr 2020 10:00:09: 2000000 INFO @ Wed, 22 Apr 2020 10:00:13: 10000000 INFO @ Wed, 22 Apr 2020 10:00:13: 3000000 INFO @ Wed, 22 Apr 2020 10:00:17: 11000000 INFO @ Wed, 22 Apr 2020 10:00:18: 4000000 INFO @ Wed, 22 Apr 2020 10:00:22: 12000000 INFO @ Wed, 22 Apr 2020 10:00:22: 5000000 INFO @ Wed, 22 Apr 2020 10:00:26: 13000000 INFO @ Wed, 22 Apr 2020 10:00:27: 6000000 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 10:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.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 10:00:30: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:00:30: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:00:30: 14000000 INFO @ Wed, 22 Apr 2020 10:00:31: 7000000 INFO @ Wed, 22 Apr 2020 10:00:34: 1000000 INFO @ Wed, 22 Apr 2020 10:00:35: 15000000 INFO @ Wed, 22 Apr 2020 10:00:36: 8000000 INFO @ Wed, 22 Apr 2020 10:00:39: 2000000 INFO @ Wed, 22 Apr 2020 10:00:39: 16000000 INFO @ Wed, 22 Apr 2020 10:00:40: 9000000 INFO @ Wed, 22 Apr 2020 10:00:43: 3000000 INFO @ Wed, 22 Apr 2020 10:00:44: 17000000 INFO @ Wed, 22 Apr 2020 10:00:45: 10000000 INFO @ Wed, 22 Apr 2020 10:00:48: 4000000 INFO @ Wed, 22 Apr 2020 10:00:48: 18000000 INFO @ Wed, 22 Apr 2020 10:00:50: 11000000 INFO @ Wed, 22 Apr 2020 10:00:52: 5000000 INFO @ Wed, 22 Apr 2020 10:00:53: 19000000 INFO @ Wed, 22 Apr 2020 10:00:54: 12000000 INFO @ Wed, 22 Apr 2020 10:00:57: 6000000 INFO @ Wed, 22 Apr 2020 10:00:57: 20000000 INFO @ Wed, 22 Apr 2020 10:00:59: 13000000 INFO @ Wed, 22 Apr 2020 10:01:01: 21000000 INFO @ Wed, 22 Apr 2020 10:01:01: 7000000 INFO @ Wed, 22 Apr 2020 10:01:03: 14000000 INFO @ Wed, 22 Apr 2020 10:01:06: 22000000 INFO @ Wed, 22 Apr 2020 10:01:06: 8000000 INFO @ Wed, 22 Apr 2020 10:01:08: 15000000 INFO @ Wed, 22 Apr 2020 10:01:10: 23000000 INFO @ Wed, 22 Apr 2020 10:01:11: 9000000 INFO @ Wed, 22 Apr 2020 10:01:12: 16000000 INFO @ Wed, 22 Apr 2020 10:01:14: 24000000 INFO @ Wed, 22 Apr 2020 10:01:15: 10000000 INFO @ Wed, 22 Apr 2020 10:01:17: 17000000 INFO @ Wed, 22 Apr 2020 10:01:19: 25000000 INFO @ Wed, 22 Apr 2020 10:01:20: 11000000 INFO @ Wed, 22 Apr 2020 10:01:21: 18000000 INFO @ Wed, 22 Apr 2020 10:01:23: 26000000 INFO @ Wed, 22 Apr 2020 10:01:24: 12000000 INFO @ Wed, 22 Apr 2020 10:01:26: 19000000 INFO @ Wed, 22 Apr 2020 10:01:28: 27000000 INFO @ Wed, 22 Apr 2020 10:01:29: 13000000 INFO @ Wed, 22 Apr 2020 10:01:30: 20000000 INFO @ Wed, 22 Apr 2020 10:01:32: 28000000 INFO @ Wed, 22 Apr 2020 10:01:33: 14000000 INFO @ Wed, 22 Apr 2020 10:01:35: 21000000 INFO @ Wed, 22 Apr 2020 10:01:36: 29000000 INFO @ Wed, 22 Apr 2020 10:01:38: 15000000 INFO @ Wed, 22 Apr 2020 10:01:39: 22000000 INFO @ Wed, 22 Apr 2020 10:01:41: 30000000 INFO @ Wed, 22 Apr 2020 10:01:42: 16000000 INFO @ Wed, 22 Apr 2020 10:01:43: 23000000 INFO @ Wed, 22 Apr 2020 10:01:45: 31000000 INFO @ Wed, 22 Apr 2020 10:01:47: 17000000 INFO @ Wed, 22 Apr 2020 10:01:48: 24000000 INFO @ Wed, 22 Apr 2020 10:01:50: 32000000 INFO @ Wed, 22 Apr 2020 10:01:51: 18000000 INFO @ Wed, 22 Apr 2020 10:01:52: 25000000 INFO @ Wed, 22 Apr 2020 10:01:54: 33000000 INFO @ Wed, 22 Apr 2020 10:01:56: 19000000 INFO @ Wed, 22 Apr 2020 10:01:57: 26000000 INFO @ Wed, 22 Apr 2020 10:01:58: 34000000 INFO @ Wed, 22 Apr 2020 10:02:00: 20000000 INFO @ Wed, 22 Apr 2020 10:02:01: 27000000 INFO @ Wed, 22 Apr 2020 10:02:03: 35000000 INFO @ Wed, 22 Apr 2020 10:02:05: 21000000 INFO @ Wed, 22 Apr 2020 10:02:06: 28000000 INFO @ Wed, 22 Apr 2020 10:02:07: 36000000 INFO @ Wed, 22 Apr 2020 10:02:09: 22000000 INFO @ Wed, 22 Apr 2020 10:02:10: 29000000 INFO @ Wed, 22 Apr 2020 10:02:11: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:02:11: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:02:11: #1 total tags in treatment: 18201927 INFO @ Wed, 22 Apr 2020 10:02:11: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:02:11: #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 10:02:11: #1 tags after filtering in treatment: 11637438 INFO @ Wed, 22 Apr 2020 10:02:11: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Apr 2020 10:02:11: #1 finished! INFO @ Wed, 22 Apr 2020 10:02:11: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:02:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:02:12: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:02:12: 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 10:02:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.05_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/SRX7409557/SRX7409557.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:02:14: 23000000 INFO @ Wed, 22 Apr 2020 10:02:15: 30000000 INFO @ Wed, 22 Apr 2020 10:02:18: 24000000 INFO @ Wed, 22 Apr 2020 10:02:19: 31000000 INFO @ Wed, 22 Apr 2020 10:02:23: 25000000 INFO @ Wed, 22 Apr 2020 10:02:24: 32000000 INFO @ Wed, 22 Apr 2020 10:02:27: 26000000 INFO @ Wed, 22 Apr 2020 10:02:28: 33000000 INFO @ Wed, 22 Apr 2020 10:02:32: 27000000 INFO @ Wed, 22 Apr 2020 10:02:33: 34000000 INFO @ Wed, 22 Apr 2020 10:02:36: 28000000 INFO @ Wed, 22 Apr 2020 10:02:37: 35000000 INFO @ Wed, 22 Apr 2020 10:02:40: 29000000 INFO @ Wed, 22 Apr 2020 10:02:41: 36000000 INFO @ Wed, 22 Apr 2020 10:02:45: 30000000 INFO @ Wed, 22 Apr 2020 10:02:45: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:02:45: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:02:45: #1 total tags in treatment: 18201927 INFO @ Wed, 22 Apr 2020 10:02:45: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:02:45: #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 10:02:45: #1 tags after filtering in treatment: 11637438 INFO @ Wed, 22 Apr 2020 10:02:45: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Apr 2020 10:02:45: #1 finished! INFO @ Wed, 22 Apr 2020 10:02:45: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:02:46: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:02:46: 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 10:02:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.10_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/SRX7409557/SRX7409557.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:02:49: 31000000 INFO @ Wed, 22 Apr 2020 10:02:54: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:02:58: 33000000 INFO @ Wed, 22 Apr 2020 10:03:02: 34000000 INFO @ Wed, 22 Apr 2020 10:03:07: 35000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:03:11: 36000000 INFO @ Wed, 22 Apr 2020 10:03:15: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:03:15: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:03:15: #1 total tags in treatment: 18201927 INFO @ Wed, 22 Apr 2020 10:03:15: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:03:15: #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 10:03:15: #1 tags after filtering in treatment: 11637438 INFO @ Wed, 22 Apr 2020 10:03:15: #1 Redundant rate of treatment: 0.36 INFO @ Wed, 22 Apr 2020 10:03:15: #1 finished! INFO @ Wed, 22 Apr 2020 10:03:15: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:03:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:03:16: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:03:16: 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 10:03:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.20_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/SRX7409557/SRX7409557.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409557/SRX7409557.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling