Job ID = 5791822 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:47:15 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 ) 2020-04-22T01:47:51 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 ) 2020-04-22T01:47:51 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 ) 2020-04-22T01:55:26 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 : 19,142,471 reads read : 38,284,942 reads written : 38,284,942 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: 00:11:41 19142471 reads; of these: 19142471 (100.00%) were paired; of these: 4955327 (25.89%) aligned concordantly 0 times 12061721 (63.01%) aligned concordantly exactly 1 time 2125423 (11.10%) aligned concordantly >1 times ---- 4955327 pairs aligned concordantly 0 times; of these: 1379360 (27.84%) aligned discordantly 1 time ---- 3575967 pairs aligned 0 times concordantly or discordantly; of these: 7151934 mates make up the pairs; of these: 6282088 (87.84%) aligned 0 times 357494 (5.00%) aligned exactly 1 time 512352 (7.16%) aligned >1 times 83.59% overall alignment rate Time searching: 00:11:41 Overall time: 00:11:41 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 16 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] 2954354 / 15459074 = 0.1911 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 11:21:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.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 11:21:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:21:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:22:01: 1000000 INFO @ Wed, 22 Apr 2020 11:22:06: 2000000 INFO @ Wed, 22 Apr 2020 11:22:12: 3000000 INFO @ Wed, 22 Apr 2020 11:22:18: 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 11:22:24: 5000000 INFO @ Wed, 22 Apr 2020 11:22:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.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 11:22:25: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:22:25: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:22:31: 6000000 INFO @ Wed, 22 Apr 2020 11:22:33: 1000000 INFO @ Wed, 22 Apr 2020 11:22:39: 7000000 INFO @ Wed, 22 Apr 2020 11:22:42: 2000000 INFO @ Wed, 22 Apr 2020 11:22:47: 8000000 INFO @ Wed, 22 Apr 2020 11:22:50: 3000000 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 11:22:54: 9000000 INFO @ Wed, 22 Apr 2020 11:22:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.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 11:22:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:22:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:22:58: 4000000 INFO @ Wed, 22 Apr 2020 11:23:02: 10000000 INFO @ Wed, 22 Apr 2020 11:23:03: 1000000 INFO @ Wed, 22 Apr 2020 11:23:07: 5000000 INFO @ Wed, 22 Apr 2020 11:23:10: 11000000 INFO @ Wed, 22 Apr 2020 11:23:11: 2000000 INFO @ Wed, 22 Apr 2020 11:23:16: 6000000 INFO @ Wed, 22 Apr 2020 11:23:18: 12000000 INFO @ Wed, 22 Apr 2020 11:23:19: 3000000 INFO @ Wed, 22 Apr 2020 11:23:25: 7000000 INFO @ Wed, 22 Apr 2020 11:23:25: 13000000 INFO @ Wed, 22 Apr 2020 11:23:26: 4000000 INFO @ Wed, 22 Apr 2020 11:23:33: 14000000 INFO @ Wed, 22 Apr 2020 11:23:34: 8000000 INFO @ Wed, 22 Apr 2020 11:23:34: 5000000 INFO @ Wed, 22 Apr 2020 11:23:41: 15000000 INFO @ Wed, 22 Apr 2020 11:23:42: 6000000 INFO @ Wed, 22 Apr 2020 11:23:42: 9000000 INFO @ Wed, 22 Apr 2020 11:23:48: 16000000 INFO @ Wed, 22 Apr 2020 11:23:49: 7000000 INFO @ Wed, 22 Apr 2020 11:23:51: 10000000 INFO @ Wed, 22 Apr 2020 11:23:56: 17000000 INFO @ Wed, 22 Apr 2020 11:23:57: 8000000 INFO @ Wed, 22 Apr 2020 11:24:00: 11000000 INFO @ Wed, 22 Apr 2020 11:24:04: 18000000 INFO @ Wed, 22 Apr 2020 11:24:05: 9000000 INFO @ Wed, 22 Apr 2020 11:24:09: 12000000 INFO @ Wed, 22 Apr 2020 11:24:12: 19000000 INFO @ Wed, 22 Apr 2020 11:24:12: 10000000 INFO @ Wed, 22 Apr 2020 11:24:18: 13000000 INFO @ Wed, 22 Apr 2020 11:24:19: 20000000 INFO @ Wed, 22 Apr 2020 11:24:20: 11000000 INFO @ Wed, 22 Apr 2020 11:24:27: 14000000 INFO @ Wed, 22 Apr 2020 11:24:27: 21000000 INFO @ Wed, 22 Apr 2020 11:24:28: 12000000 INFO @ Wed, 22 Apr 2020 11:24:36: 15000000 INFO @ Wed, 22 Apr 2020 11:24:36: 13000000 INFO @ Wed, 22 Apr 2020 11:24:36: 22000000 INFO @ Wed, 22 Apr 2020 11:24:43: 16000000 INFO @ Wed, 22 Apr 2020 11:24:43: 14000000 INFO @ Wed, 22 Apr 2020 11:24:43: 23000000 INFO @ Wed, 22 Apr 2020 11:24:51: 15000000 INFO @ Wed, 22 Apr 2020 11:24:51: 24000000 INFO @ Wed, 22 Apr 2020 11:24:51: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:24:58: 16000000 INFO @ Wed, 22 Apr 2020 11:24:59: 25000000 INFO @ Wed, 22 Apr 2020 11:25:00: 18000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 11:25:06: 17000000 INFO @ Wed, 22 Apr 2020 11:25:06: 26000000 INFO @ Wed, 22 Apr 2020 11:25:07: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:25:07: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:25:07: #1 total tags in treatment: 11456265 INFO @ Wed, 22 Apr 2020 11:25:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:25:07: #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 11:25:07: #1 tags after filtering in treatment: 5221287 INFO @ Wed, 22 Apr 2020 11:25:07: #1 Redundant rate of treatment: 0.54 INFO @ Wed, 22 Apr 2020 11:25:07: #1 finished! INFO @ Wed, 22 Apr 2020 11:25:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:25:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:25:07: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:25:07: 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 11:25:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.05_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/SRX7756602/SRX7756602.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:25:08: 19000000 INFO @ Wed, 22 Apr 2020 11:25:14: 18000000 INFO @ Wed, 22 Apr 2020 11:25:17: 20000000 INFO @ Wed, 22 Apr 2020 11:25:21: 19000000 INFO @ Wed, 22 Apr 2020 11:25:26: 21000000 INFO @ Wed, 22 Apr 2020 11:25:29: 20000000 INFO @ Wed, 22 Apr 2020 11:25:35: 22000000 INFO @ Wed, 22 Apr 2020 11:25:37: 21000000 INFO @ Wed, 22 Apr 2020 11:25:44: 23000000 INFO @ Wed, 22 Apr 2020 11:25:44: 22000000 INFO @ Wed, 22 Apr 2020 11:25:52: 23000000 INFO @ Wed, 22 Apr 2020 11:25:53: 24000000 INFO @ Wed, 22 Apr 2020 11:26:00: 24000000 INFO @ Wed, 22 Apr 2020 11:26:02: 25000000 INFO @ Wed, 22 Apr 2020 11:26:07: 25000000 INFO @ Wed, 22 Apr 2020 11:26:11: 26000000 INFO @ Wed, 22 Apr 2020 11:26:11: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:26:11: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:26:11: #1 total tags in treatment: 11456265 INFO @ Wed, 22 Apr 2020 11:26:11: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:26:11: #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 11:26:12: #1 tags after filtering in treatment: 5221287 INFO @ Wed, 22 Apr 2020 11:26:12: #1 Redundant rate of treatment: 0.54 INFO @ Wed, 22 Apr 2020 11:26:12: #1 finished! INFO @ Wed, 22 Apr 2020 11:26:12: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:26:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:26:12: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:26:12: 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 11:26:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.10_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/SRX7756602/SRX7756602.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:26:14: 26000000 INFO @ Wed, 22 Apr 2020 11:26:15: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:26:15: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:26:15: #1 total tags in treatment: 11456265 INFO @ Wed, 22 Apr 2020 11:26:15: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:26:15: #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 11:26:15: #1 tags after filtering in treatment: 5221287 INFO @ Wed, 22 Apr 2020 11:26:15: #1 Redundant rate of treatment: 0.54 INFO @ Wed, 22 Apr 2020 11:26:15: #1 finished! INFO @ Wed, 22 Apr 2020 11:26:15: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:26:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:26:16: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:26:16: 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 11:26:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.20_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/SRX7756602/SRX7756602.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756602/SRX7756602.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling