Job ID = 5791677 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:22:40 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 ) 2020-04-22T01:22:40 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 ) 2020-04-22T01:33:42 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 ) 2020-04-22T01:33:42 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 ) 2020-04-22T01:43:16 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 ) 2020-04-22T01:43:16 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 ) 2020-04-22T01:43:23 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 ) 2020-04-22T01:43:23 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 : 16,999,504 reads read : 33,999,008 reads written : 33,999,008 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: 00:19:15 16999504 reads; of these: 16999504 (100.00%) were paired; of these: 7359674 (43.29%) aligned concordantly 0 times 7920787 (46.59%) aligned concordantly exactly 1 time 1719043 (10.11%) aligned concordantly >1 times ---- 7359674 pairs aligned concordantly 0 times; of these: 1499009 (20.37%) aligned discordantly 1 time ---- 5860665 pairs aligned 0 times concordantly or discordantly; of these: 11721330 mates make up the pairs; of these: 10488771 (89.48%) aligned 0 times 476052 (4.06%) aligned exactly 1 time 756507 (6.45%) aligned >1 times 69.15% overall alignment rate Time searching: 00:19:15 Overall time: 00:19:15 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] 4508152 / 11054618 = 0.4078 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 11:24:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.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 11:24:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:24:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:24:31: 1000000 INFO @ Wed, 22 Apr 2020 11:24:38: 2000000 INFO @ Wed, 22 Apr 2020 11:24:45: 3000000 INFO @ Wed, 22 Apr 2020 11:24:52: 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 11:24:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.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 11:24:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:24:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:24:59: 5000000 INFO @ Wed, 22 Apr 2020 11:25:02: 1000000 INFO @ Wed, 22 Apr 2020 11:25:07: 6000000 INFO @ Wed, 22 Apr 2020 11:25:09: 2000000 INFO @ Wed, 22 Apr 2020 11:25:14: 7000000 INFO @ Wed, 22 Apr 2020 11:25:16: 3000000 INFO @ Wed, 22 Apr 2020 11:25:22: 8000000 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 11:25:24: 4000000 INFO @ Wed, 22 Apr 2020 11:25:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.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 11:25:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:25:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:25:29: 9000000 INFO @ Wed, 22 Apr 2020 11:25:31: 5000000 INFO @ Wed, 22 Apr 2020 11:25:33: 1000000 INFO @ Wed, 22 Apr 2020 11:25:37: 10000000 INFO @ Wed, 22 Apr 2020 11:25:39: 6000000 INFO @ Wed, 22 Apr 2020 11:25:42: 2000000 INFO @ Wed, 22 Apr 2020 11:25:44: 11000000 INFO @ Wed, 22 Apr 2020 11:25:47: 7000000 INFO @ Wed, 22 Apr 2020 11:25:51: 3000000 INFO @ Wed, 22 Apr 2020 11:25:52: 12000000 INFO @ Wed, 22 Apr 2020 11:25:55: 8000000 INFO @ Wed, 22 Apr 2020 11:25:59: 13000000 INFO @ Wed, 22 Apr 2020 11:25:59: 4000000 INFO @ Wed, 22 Apr 2020 11:26:03: 9000000 INFO @ Wed, 22 Apr 2020 11:26:07: 14000000 INFO @ Wed, 22 Apr 2020 11:26:08: 5000000 INFO @ Wed, 22 Apr 2020 11:26:10: 10000000 INFO @ Wed, 22 Apr 2020 11:26:10: #1 tag size is determined as 150 bps INFO @ Wed, 22 Apr 2020 11:26:10: #1 tag size = 150 INFO @ Wed, 22 Apr 2020 11:26:10: #1 total tags in treatment: 5546769 INFO @ Wed, 22 Apr 2020 11:26:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:26:10: #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 11:26:10: #1 tags after filtering in treatment: 4206267 INFO @ Wed, 22 Apr 2020 11:26:10: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 11:26:10: #1 finished! INFO @ Wed, 22 Apr 2020 11:26:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:26:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:26:11: #2 number of paired peaks: 33 WARNING @ Wed, 22 Apr 2020 11:26:11: Too few paired peaks (33) 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 11:26:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.05_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/SRX7409637/SRX7409637.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:26:17: 6000000 INFO @ Wed, 22 Apr 2020 11:26:18: 11000000 INFO @ Wed, 22 Apr 2020 11:26:25: 12000000 INFO @ Wed, 22 Apr 2020 11:26:26: 7000000 INFO @ Wed, 22 Apr 2020 11:26:32: 13000000 INFO @ Wed, 22 Apr 2020 11:26:34: 8000000 INFO @ Wed, 22 Apr 2020 11:26:40: 14000000 INFO @ Wed, 22 Apr 2020 11:26:43: 9000000 INFO @ Wed, 22 Apr 2020 11:26:43: #1 tag size is determined as 150 bps INFO @ Wed, 22 Apr 2020 11:26:43: #1 tag size = 150 INFO @ Wed, 22 Apr 2020 11:26:43: #1 total tags in treatment: 5546769 INFO @ Wed, 22 Apr 2020 11:26:43: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:26:43: #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 11:26:44: #1 tags after filtering in treatment: 4206267 INFO @ Wed, 22 Apr 2020 11:26:44: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 11:26:44: #1 finished! INFO @ Wed, 22 Apr 2020 11:26:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:26:44: #2 number of paired peaks: 33 WARNING @ Wed, 22 Apr 2020 11:26:44: Too few paired peaks (33) 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 11:26:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.10_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/SRX7409637/SRX7409637.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:26:52: 10000000 INFO @ Wed, 22 Apr 2020 11:27:00: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:27:08: 12000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 11:27:17: 13000000 INFO @ Wed, 22 Apr 2020 11:27:25: 14000000 INFO @ Wed, 22 Apr 2020 11:27:29: #1 tag size is determined as 150 bps INFO @ Wed, 22 Apr 2020 11:27:29: #1 tag size = 150 INFO @ Wed, 22 Apr 2020 11:27:29: #1 total tags in treatment: 5546769 INFO @ Wed, 22 Apr 2020 11:27:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:27:29: #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 11:27:29: #1 tags after filtering in treatment: 4206267 INFO @ Wed, 22 Apr 2020 11:27:29: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 11:27:29: #1 finished! INFO @ Wed, 22 Apr 2020 11:27:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:27:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:27:30: #2 number of paired peaks: 33 WARNING @ Wed, 22 Apr 2020 11:27:30: Too few paired peaks (33) 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 11:27:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409637/SRX7409637.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling