Job ID = 5791285 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:20:42 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 ) 2020-04-22T00:21:50 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 ) 2020-04-22T00:21:50 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 ) 2020-04-22T00:26:39 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 ) 2020-04-22T00:26:39 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 ) 2020-04-22T00:28:08 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 ) 2020-04-22T00:29:48 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 ) 2020-04-22T00:29:48 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 ) 2020-04-22T00:36:15 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 ) 2020-04-22T00:36:15 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 : 31,703,359 reads read : 63,406,718 reads written : 63,406,718 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: 00:10:51 31703359 reads; of these: 31703359 (100.00%) were paired; of these: 11352566 (35.81%) aligned concordantly 0 times 18323915 (57.80%) aligned concordantly exactly 1 time 2026878 (6.39%) aligned concordantly >1 times ---- 11352566 pairs aligned concordantly 0 times; of these: 48778 (0.43%) aligned discordantly 1 time ---- 11303788 pairs aligned 0 times concordantly or discordantly; of these: 22607576 mates make up the pairs; of these: 22167278 (98.05%) aligned 0 times 382046 (1.69%) aligned exactly 1 time 58252 (0.26%) aligned >1 times 65.04% overall alignment rate Time searching: 00:10:51 Overall time: 00:10:51 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] 9855993 / 20360906 = 0.4841 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 10:00:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.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 10:00:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:00:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:00:30: 1000000 INFO @ Wed, 22 Apr 2020 10:00:35: 2000000 INFO @ Wed, 22 Apr 2020 10:00:41: 3000000 INFO @ Wed, 22 Apr 2020 10:00:47: 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 10:00:54: 5000000 INFO @ Wed, 22 Apr 2020 10:00:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.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 10:00:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:00:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:01:00: 1000000 INFO @ Wed, 22 Apr 2020 10:01:00: 6000000 INFO @ Wed, 22 Apr 2020 10:01:05: 2000000 INFO @ Wed, 22 Apr 2020 10:01:06: 7000000 INFO @ Wed, 22 Apr 2020 10:01:11: 3000000 INFO @ Wed, 22 Apr 2020 10:01:12: 8000000 INFO @ Wed, 22 Apr 2020 10:01:17: 4000000 INFO @ Wed, 22 Apr 2020 10:01:19: 9000000 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 10:01:22: 5000000 INFO @ Wed, 22 Apr 2020 10:01:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.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 10:01:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:01:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:01:26: 10000000 INFO @ Wed, 22 Apr 2020 10:01:27: 6000000 INFO @ Wed, 22 Apr 2020 10:01:29: 1000000 INFO @ Wed, 22 Apr 2020 10:01:32: 11000000 INFO @ Wed, 22 Apr 2020 10:01:33: 7000000 INFO @ Wed, 22 Apr 2020 10:01:34: 2000000 INFO @ Wed, 22 Apr 2020 10:01:38: 12000000 INFO @ Wed, 22 Apr 2020 10:01:39: 3000000 INFO @ Wed, 22 Apr 2020 10:01:40: 8000000 INFO @ Wed, 22 Apr 2020 10:01:44: 4000000 INFO @ Wed, 22 Apr 2020 10:01:44: 13000000 INFO @ Wed, 22 Apr 2020 10:01:46: 9000000 INFO @ Wed, 22 Apr 2020 10:01:49: 5000000 INFO @ Wed, 22 Apr 2020 10:01:50: 14000000 INFO @ Wed, 22 Apr 2020 10:01:52: 10000000 INFO @ Wed, 22 Apr 2020 10:01:54: 6000000 INFO @ Wed, 22 Apr 2020 10:01:56: 15000000 INFO @ Wed, 22 Apr 2020 10:01:58: 11000000 INFO @ Wed, 22 Apr 2020 10:01:59: 7000000 INFO @ Wed, 22 Apr 2020 10:02:02: 16000000 INFO @ Wed, 22 Apr 2020 10:02:04: 12000000 INFO @ Wed, 22 Apr 2020 10:02:04: 8000000 INFO @ Wed, 22 Apr 2020 10:02:08: 17000000 INFO @ Wed, 22 Apr 2020 10:02:09: 9000000 INFO @ Wed, 22 Apr 2020 10:02:13: 18000000 INFO @ Wed, 22 Apr 2020 10:02:14: 10000000 INFO @ Wed, 22 Apr 2020 10:02:19: 11000000 INFO @ Wed, 22 Apr 2020 10:02:21: 19000000 INFO @ Wed, 22 Apr 2020 10:02:24: 12000000 INFO @ Wed, 22 Apr 2020 10:02:26: 13000000 INFO @ Wed, 22 Apr 2020 10:02:28: 20000000 INFO @ Wed, 22 Apr 2020 10:02:29: 13000000 INFO @ Wed, 22 Apr 2020 10:02:34: 14000000 INFO @ Wed, 22 Apr 2020 10:02:35: 21000000 INFO @ Wed, 22 Apr 2020 10:02:37: 14000000 INFO @ Wed, 22 Apr 2020 10:02:39: 15000000 INFO @ Wed, 22 Apr 2020 10:02:39: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:02:39: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:02:39: #1 total tags in treatment: 10498468 INFO @ Wed, 22 Apr 2020 10:02:39: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:02:39: #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 10:02:39: #1 tags after filtering in treatment: 7985825 INFO @ Wed, 22 Apr 2020 10:02:39: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 10:02:39: #1 finished! INFO @ Wed, 22 Apr 2020 10:02:39: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:02:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:02:40: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:02:40: 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 10:02:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.05_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/SRX7409544/SRX7409544.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:02:44: 16000000 INFO @ Wed, 22 Apr 2020 10:02:46: 15000000 INFO @ Wed, 22 Apr 2020 10:02:48: 17000000 INFO @ Wed, 22 Apr 2020 10:02:53: 18000000 INFO @ Wed, 22 Apr 2020 10:02:55: 16000000 INFO @ Wed, 22 Apr 2020 10:02:58: 19000000 INFO @ Wed, 22 Apr 2020 10:03:01: 17000000 INFO @ Wed, 22 Apr 2020 10:03:03: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:03:07: 18000000 INFO @ Wed, 22 Apr 2020 10:03:08: 21000000 INFO @ Wed, 22 Apr 2020 10:03:11: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:03:11: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:03:11: #1 total tags in treatment: 10498468 INFO @ Wed, 22 Apr 2020 10:03:11: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:03:11: #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 10:03:11: #1 tags after filtering in treatment: 7985825 INFO @ Wed, 22 Apr 2020 10:03:11: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 10:03:11: #1 finished! INFO @ Wed, 22 Apr 2020 10:03:11: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:03:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:03:11: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:03:11: 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 10:03:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.20_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/SRX7409544/SRX7409544.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:03:13: 19000000 INFO @ Wed, 22 Apr 2020 10:03:18: 20000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:03:24: 21000000 INFO @ Wed, 22 Apr 2020 10:03:26: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:03:26: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:03:26: #1 total tags in treatment: 10498468 INFO @ Wed, 22 Apr 2020 10:03:26: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:03:26: #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 10:03:27: #1 tags after filtering in treatment: 7985825 INFO @ Wed, 22 Apr 2020 10:03:27: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 10:03:27: #1 finished! INFO @ Wed, 22 Apr 2020 10:03:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:03:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:03:27: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:03:27: 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 10:03:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.10_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/SRX7409544/SRX7409544.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409544/SRX7409544.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling