Job ID = 5720332 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T14:25:11 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 ) 2020-04-15T14:27:56 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 ) 2020-04-15T14:36:47 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 ) 2020-04-15T14:36:47 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 ) 2020-04-15T14:36:47 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 ) 2020-04-15T14:36:47 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 : 35,864,156 reads read : 35,864,156 reads written : 35,864,156 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: 00:11:08 35864156 reads; of these: 35864156 (100.00%) were unpaired; of these: 831814 (2.32%) aligned 0 times 29335273 (81.80%) aligned exactly 1 time 5697069 (15.89%) aligned >1 times 97.68% overall alignment rate Time searching: 00:11:08 Overall time: 00:11:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 4757443 / 35032342 = 0.1358 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 @ Thu, 16 Apr 2020 00:12:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 16 Apr 2020 00:12:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:12:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:13:02: 1000000 INFO @ Thu, 16 Apr 2020 00:13:08: 2000000 INFO @ Thu, 16 Apr 2020 00:13:14: 3000000 INFO @ Thu, 16 Apr 2020 00:13:20: 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 @ Thu, 16 Apr 2020 00:13:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 16 Apr 2020 00:13:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:13:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:13:26: 5000000 INFO @ Thu, 16 Apr 2020 00:13:32: 1000000 INFO @ Thu, 16 Apr 2020 00:13:33: 6000000 INFO @ Thu, 16 Apr 2020 00:13:39: 2000000 INFO @ Thu, 16 Apr 2020 00:13:39: 7000000 INFO @ Thu, 16 Apr 2020 00:13:45: 3000000 INFO @ Thu, 16 Apr 2020 00:13:45: 8000000 INFO @ Thu, 16 Apr 2020 00:13:51: 4000000 INFO @ Thu, 16 Apr 2020 00:13:52: 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 @ Thu, 16 Apr 2020 00:13:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 16 Apr 2020 00:13:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:13:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:13:58: 5000000 INFO @ Thu, 16 Apr 2020 00:13:58: 10000000 INFO @ Thu, 16 Apr 2020 00:14:04: 1000000 INFO @ Thu, 16 Apr 2020 00:14:05: 6000000 INFO @ Thu, 16 Apr 2020 00:14:06: 11000000 INFO @ Thu, 16 Apr 2020 00:14:11: 2000000 INFO @ Thu, 16 Apr 2020 00:14:12: 7000000 INFO @ Thu, 16 Apr 2020 00:14:13: 12000000 INFO @ Thu, 16 Apr 2020 00:14:19: 3000000 INFO @ Thu, 16 Apr 2020 00:14:19: 8000000 INFO @ Thu, 16 Apr 2020 00:14:20: 13000000 INFO @ Thu, 16 Apr 2020 00:14:26: 9000000 INFO @ Thu, 16 Apr 2020 00:14:27: 4000000 INFO @ Thu, 16 Apr 2020 00:14:27: 14000000 INFO @ Thu, 16 Apr 2020 00:14:33: 10000000 INFO @ Thu, 16 Apr 2020 00:14:34: 15000000 INFO @ Thu, 16 Apr 2020 00:14:34: 5000000 INFO @ Thu, 16 Apr 2020 00:14:40: 11000000 INFO @ Thu, 16 Apr 2020 00:14:41: 16000000 INFO @ Thu, 16 Apr 2020 00:14:42: 6000000 INFO @ Thu, 16 Apr 2020 00:14:47: 12000000 INFO @ Thu, 16 Apr 2020 00:14:48: 17000000 INFO @ Thu, 16 Apr 2020 00:14:49: 7000000 INFO @ Thu, 16 Apr 2020 00:14:54: 13000000 INFO @ Thu, 16 Apr 2020 00:14:55: 18000000 INFO @ Thu, 16 Apr 2020 00:14:57: 8000000 INFO @ Thu, 16 Apr 2020 00:15:01: 14000000 INFO @ Thu, 16 Apr 2020 00:15:02: 19000000 INFO @ Thu, 16 Apr 2020 00:15:05: 9000000 INFO @ Thu, 16 Apr 2020 00:15:08: 15000000 INFO @ Thu, 16 Apr 2020 00:15:09: 20000000 INFO @ Thu, 16 Apr 2020 00:15:12: 10000000 INFO @ Thu, 16 Apr 2020 00:15:15: 16000000 INFO @ Thu, 16 Apr 2020 00:15:16: 21000000 INFO @ Thu, 16 Apr 2020 00:15:20: 11000000 INFO @ Thu, 16 Apr 2020 00:15:23: 17000000 INFO @ Thu, 16 Apr 2020 00:15:23: 22000000 INFO @ Thu, 16 Apr 2020 00:15:27: 12000000 INFO @ Thu, 16 Apr 2020 00:15:29: 18000000 INFO @ Thu, 16 Apr 2020 00:15:30: 23000000 INFO @ Thu, 16 Apr 2020 00:15:35: 13000000 INFO @ Thu, 16 Apr 2020 00:15:37: 19000000 INFO @ Thu, 16 Apr 2020 00:15:37: 24000000 INFO @ Thu, 16 Apr 2020 00:15:43: 14000000 INFO @ Thu, 16 Apr 2020 00:15:44: 20000000 INFO @ Thu, 16 Apr 2020 00:15:44: 25000000 INFO @ Thu, 16 Apr 2020 00:15:50: 15000000 INFO @ Thu, 16 Apr 2020 00:15:51: 21000000 INFO @ Thu, 16 Apr 2020 00:15:52: 26000000 INFO @ Thu, 16 Apr 2020 00:15:58: 22000000 INFO @ Thu, 16 Apr 2020 00:15:58: 16000000 INFO @ Thu, 16 Apr 2020 00:15:59: 27000000 INFO @ Thu, 16 Apr 2020 00:16:04: 23000000 INFO @ Thu, 16 Apr 2020 00:16:05: 17000000 INFO @ Thu, 16 Apr 2020 00:16:06: 28000000 INFO @ Thu, 16 Apr 2020 00:16:11: 24000000 INFO @ Thu, 16 Apr 2020 00:16:13: 18000000 INFO @ Thu, 16 Apr 2020 00:16:13: 29000000 INFO @ Thu, 16 Apr 2020 00:16:18: 25000000 INFO @ Thu, 16 Apr 2020 00:16:20: 30000000 INFO @ Thu, 16 Apr 2020 00:16:20: 19000000 INFO @ Thu, 16 Apr 2020 00:16:22: #1 tag size is determined as 76 bps INFO @ Thu, 16 Apr 2020 00:16:22: #1 tag size = 76 INFO @ Thu, 16 Apr 2020 00:16:22: #1 total tags in treatment: 30274899 INFO @ Thu, 16 Apr 2020 00:16:22: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:16:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:16:22: #1 tags after filtering in treatment: 30274899 INFO @ Thu, 16 Apr 2020 00:16:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:16:22: #1 finished! INFO @ Thu, 16 Apr 2020 00:16:22: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:16:24: #2 number of paired peaks: 72 WARNING @ Thu, 16 Apr 2020 00:16:24: Too few paired peaks (72) 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 @ Thu, 16 Apr 2020 00:16:24: Process for pairing-model is terminated! INFO @ Thu, 16 Apr 2020 00:16:25: 26000000 INFO @ Thu, 16 Apr 2020 00:16:28: 20000000 cut: /home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.05_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/ce10/SRX7971798/SRX7971798.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:16:32: 27000000 INFO @ Thu, 16 Apr 2020 00:16:35: 21000000 INFO @ Thu, 16 Apr 2020 00:16:39: 28000000 INFO @ Thu, 16 Apr 2020 00:16:42: 22000000 INFO @ Thu, 16 Apr 2020 00:16:45: 29000000 INFO @ Thu, 16 Apr 2020 00:16:50: 23000000 INFO @ Thu, 16 Apr 2020 00:16:52: 30000000 INFO @ Thu, 16 Apr 2020 00:16:54: #1 tag size is determined as 76 bps INFO @ Thu, 16 Apr 2020 00:16:54: #1 tag size = 76 INFO @ Thu, 16 Apr 2020 00:16:54: #1 total tags in treatment: 30274899 INFO @ Thu, 16 Apr 2020 00:16:54: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:16:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:16:54: #1 tags after filtering in treatment: 30274899 INFO @ Thu, 16 Apr 2020 00:16:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:16:54: #1 finished! INFO @ Thu, 16 Apr 2020 00:16:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:16:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:16:56: #2 number of paired peaks: 72 WARNING @ Thu, 16 Apr 2020 00:16:56: Too few paired peaks (72) 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 @ Thu, 16 Apr 2020 00:16:56: Process for pairing-model is terminated! INFO @ Thu, 16 Apr 2020 00:16:57: 24000000 cut: /home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.10_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/ce10/SRX7971798/SRX7971798.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:17:04: 25000000 INFO @ Thu, 16 Apr 2020 00:17:11: 26000000 INFO @ Thu, 16 Apr 2020 00:17:19: 27000000 INFO @ Thu, 16 Apr 2020 00:17:26: 28000000 INFO @ Thu, 16 Apr 2020 00:17:33: 29000000 INFO @ Thu, 16 Apr 2020 00:17:40: 30000000 INFO @ Thu, 16 Apr 2020 00:17:42: #1 tag size is determined as 76 bps INFO @ Thu, 16 Apr 2020 00:17:42: #1 tag size = 76 INFO @ Thu, 16 Apr 2020 00:17:42: #1 total tags in treatment: 30274899 INFO @ Thu, 16 Apr 2020 00:17:42: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:17:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:17:42: #1 tags after filtering in treatment: 30274899 INFO @ Thu, 16 Apr 2020 00:17:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:17:42: #1 finished! INFO @ Thu, 16 Apr 2020 00:17:42: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:17:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:17:44: #2 number of paired peaks: 72 WARNING @ Thu, 16 Apr 2020 00:17:44: Too few paired peaks (72) 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 @ Thu, 16 Apr 2020 00:17:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.20_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/ce10/SRX7971798/SRX7971798.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/ce10/SRX7971798/SRX7971798.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。