Job ID = 5791571 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:58:52 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 ) 2020-04-22T00:58:52 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 : 33,232,184 reads read : 66,464,368 reads written : 66,464,368 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: 00:21:42 33232184 reads; of these: 33232184 (100.00%) were paired; of these: 3080997 (9.27%) aligned concordantly 0 times 26678387 (80.28%) aligned concordantly exactly 1 time 3472800 (10.45%) aligned concordantly >1 times ---- 3080997 pairs aligned concordantly 0 times; of these: 55613 (1.81%) aligned discordantly 1 time ---- 3025384 pairs aligned 0 times concordantly or discordantly; of these: 6050768 mates make up the pairs; of these: 5774423 (95.43%) aligned 0 times 219925 (3.63%) aligned exactly 1 time 56420 (0.93%) aligned >1 times 91.31% overall alignment rate Time searching: 00:21:42 Overall time: 00:21:42 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 28 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] 22052874 / 30160284 = 0.7312 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 10:32:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.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 10:32:16: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:32:16: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:32:22: 1000000 INFO @ Wed, 22 Apr 2020 10:32:27: 2000000 INFO @ Wed, 22 Apr 2020 10:32:33: 3000000 INFO @ Wed, 22 Apr 2020 10:32:39: 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 10:32:44: 5000000 INFO @ Wed, 22 Apr 2020 10:32:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.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 10:32:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:32:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:32:50: 6000000 INFO @ Wed, 22 Apr 2020 10:32:56: 7000000 INFO @ Wed, 22 Apr 2020 10:32:57: 1000000 INFO @ Wed, 22 Apr 2020 10:33:02: 8000000 INFO @ Wed, 22 Apr 2020 10:33:05: 2000000 INFO @ Wed, 22 Apr 2020 10:33:09: 9000000 INFO @ Wed, 22 Apr 2020 10:33:13: 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 10:33:15: 10000000 INFO @ Wed, 22 Apr 2020 10:33:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.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 10:33:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:33:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:33:21: 4000000 INFO @ Wed, 22 Apr 2020 10:33:21: 11000000 INFO @ Wed, 22 Apr 2020 10:33:23: 1000000 INFO @ Wed, 22 Apr 2020 10:33:27: 12000000 INFO @ Wed, 22 Apr 2020 10:33:29: 5000000 INFO @ Wed, 22 Apr 2020 10:33:29: 2000000 INFO @ Wed, 22 Apr 2020 10:33:33: 13000000 INFO @ Wed, 22 Apr 2020 10:33:35: 3000000 INFO @ Wed, 22 Apr 2020 10:33:37: 6000000 INFO @ Wed, 22 Apr 2020 10:33:40: 14000000 INFO @ Wed, 22 Apr 2020 10:33:41: 4000000 INFO @ Wed, 22 Apr 2020 10:33:44: 7000000 INFO @ Wed, 22 Apr 2020 10:33:46: 15000000 INFO @ Wed, 22 Apr 2020 10:33:47: 5000000 INFO @ Wed, 22 Apr 2020 10:33:50: 8000000 INFO @ Wed, 22 Apr 2020 10:33:52: 16000000 INFO @ Wed, 22 Apr 2020 10:33:53: 6000000 INFO @ Wed, 22 Apr 2020 10:33:55: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:33:55: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:33:55: #1 total tags in treatment: 8103352 INFO @ Wed, 22 Apr 2020 10:33:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:33:55: #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 10:33:55: #1 tags after filtering in treatment: 6242179 INFO @ Wed, 22 Apr 2020 10:33:55: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Apr 2020 10:33:55: #1 finished! INFO @ Wed, 22 Apr 2020 10:33:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:33:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:33:56: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:33:56: 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 10:33:56: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:33:56: 9000000 INFO @ Wed, 22 Apr 2020 10:33:59: 7000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.05_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/SRX7409585/SRX7409585.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:34:02: 10000000 INFO @ Wed, 22 Apr 2020 10:34:05: 8000000 INFO @ Wed, 22 Apr 2020 10:34:08: 11000000 INFO @ Wed, 22 Apr 2020 10:34:11: 9000000 INFO @ Wed, 22 Apr 2020 10:34:14: 12000000 INFO @ Wed, 22 Apr 2020 10:34:16: 10000000 INFO @ Wed, 22 Apr 2020 10:34:20: 13000000 INFO @ Wed, 22 Apr 2020 10:34:22: 11000000 INFO @ Wed, 22 Apr 2020 10:34:25: 14000000 INFO @ Wed, 22 Apr 2020 10:34:28: 12000000 INFO @ Wed, 22 Apr 2020 10:34:31: 15000000 INFO @ Wed, 22 Apr 2020 10:34:34: 13000000 INFO @ Wed, 22 Apr 2020 10:34:37: 16000000 INFO @ Wed, 22 Apr 2020 10:34:40: 14000000 INFO @ Wed, 22 Apr 2020 10:34:41: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:34:41: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:34:41: #1 total tags in treatment: 8103352 INFO @ Wed, 22 Apr 2020 10:34:41: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:34:41: #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 10:34:41: #1 tags after filtering in treatment: 6242179 INFO @ Wed, 22 Apr 2020 10:34:41: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Apr 2020 10:34:41: #1 finished! INFO @ Wed, 22 Apr 2020 10:34:41: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:34:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:34:41: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:34:41: 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 10:34:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.10_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/SRX7409585/SRX7409585.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:34:45: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:34:51: 16000000 INFO @ Wed, 22 Apr 2020 10:34:54: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:34:54: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:34:54: #1 total tags in treatment: 8103352 INFO @ Wed, 22 Apr 2020 10:34:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:34:54: #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 10:34:54: #1 tags after filtering in treatment: 6242179 INFO @ Wed, 22 Apr 2020 10:34:54: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Apr 2020 10:34:54: #1 finished! INFO @ Wed, 22 Apr 2020 10:34:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:34:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:34:55: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:34:55: 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 10:34:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.20_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/SRX7409585/SRX7409585.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409585/SRX7409585.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。