Job ID = 5791281 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:26:07 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 ) 2020-04-22T00:26:07 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 ) 2020-04-22T00:34:54 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 ) 2020-04-22T00:34:54 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 : 40,384,971 reads read : 80,769,942 reads written : 80,769,942 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: 00:10:46 40384971 reads; of these: 40384971 (100.00%) were paired; of these: 22004314 (54.49%) aligned concordantly 0 times 16635419 (41.19%) aligned concordantly exactly 1 time 1745238 (4.32%) aligned concordantly >1 times ---- 22004314 pairs aligned concordantly 0 times; of these: 41812 (0.19%) aligned discordantly 1 time ---- 21962502 pairs aligned 0 times concordantly or discordantly; of these: 43925004 mates make up the pairs; of these: 43458516 (98.94%) aligned 0 times 408816 (0.93%) aligned exactly 1 time 57672 (0.13%) aligned >1 times 46.19% overall alignment rate Time searching: 00:10:46 Overall time: 00:10:46 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] 10473906 / 18392145 = 0.5695 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 10:02:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.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 10:02:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:02:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:02:28: 1000000 INFO @ Wed, 22 Apr 2020 10:02:32: 2000000 INFO @ Wed, 22 Apr 2020 10:02:36: 3000000 INFO @ Wed, 22 Apr 2020 10:02:40: 4000000 INFO @ Wed, 22 Apr 2020 10:02:44: 5000000 INFO @ Wed, 22 Apr 2020 10:02:48: 6000000 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 10:02:52: 7000000 INFO @ Wed, 22 Apr 2020 10:02:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.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 10:02:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:02:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:02:56: 8000000 INFO @ Wed, 22 Apr 2020 10:02:58: 1000000 INFO @ Wed, 22 Apr 2020 10:03:00: 9000000 INFO @ Wed, 22 Apr 2020 10:03:02: 2000000 INFO @ Wed, 22 Apr 2020 10:03:04: 10000000 INFO @ Wed, 22 Apr 2020 10:03:06: 3000000 INFO @ Wed, 22 Apr 2020 10:03:09: 11000000 INFO @ Wed, 22 Apr 2020 10:03:10: 4000000 INFO @ Wed, 22 Apr 2020 10:03:13: 12000000 INFO @ Wed, 22 Apr 2020 10:03:15: 5000000 INFO @ Wed, 22 Apr 2020 10:03:17: 13000000 INFO @ Wed, 22 Apr 2020 10:03:19: 6000000 INFO @ Wed, 22 Apr 2020 10:03:21: 14000000 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 10:03:23: 7000000 INFO @ Wed, 22 Apr 2020 10:03:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.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 10:03:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:03:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:03:25: 15000000 INFO @ Wed, 22 Apr 2020 10:03:27: 8000000 INFO @ Wed, 22 Apr 2020 10:03:28: 1000000 INFO @ Wed, 22 Apr 2020 10:03:29: 16000000 INFO @ Wed, 22 Apr 2020 10:03:31: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:03:31: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:03:31: #1 total tags in treatment: 7911301 INFO @ Wed, 22 Apr 2020 10:03:31: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:03:31: #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 10:03:31: #1 tags after filtering in treatment: 6386539 INFO @ Wed, 22 Apr 2020 10:03:31: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 10:03:31: #1 finished! INFO @ Wed, 22 Apr 2020 10:03:31: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:03:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:03:31: 9000000 INFO @ Wed, 22 Apr 2020 10:03:31: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:03:31: 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 10:03:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.05_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/SRX7409540/SRX7409540.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:03:32: 2000000 INFO @ Wed, 22 Apr 2020 10:03:35: 10000000 INFO @ Wed, 22 Apr 2020 10:03:37: 3000000 INFO @ Wed, 22 Apr 2020 10:03:39: 11000000 INFO @ Wed, 22 Apr 2020 10:03:41: 4000000 INFO @ Wed, 22 Apr 2020 10:03:43: 12000000 INFO @ Wed, 22 Apr 2020 10:03:45: 5000000 INFO @ Wed, 22 Apr 2020 10:03:47: 13000000 INFO @ Wed, 22 Apr 2020 10:03:49: 6000000 INFO @ Wed, 22 Apr 2020 10:03:52: 14000000 INFO @ Wed, 22 Apr 2020 10:03:53: 7000000 INFO @ Wed, 22 Apr 2020 10:03:56: 15000000 INFO @ Wed, 22 Apr 2020 10:03:57: 8000000 INFO @ Wed, 22 Apr 2020 10:04:00: 16000000 INFO @ Wed, 22 Apr 2020 10:04:01: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:04:01: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:04:01: #1 total tags in treatment: 7911301 INFO @ Wed, 22 Apr 2020 10:04:01: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:04:01: #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 10:04:01: #1 tags after filtering in treatment: 6386539 INFO @ Wed, 22 Apr 2020 10:04:01: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 10:04:01: #1 finished! INFO @ Wed, 22 Apr 2020 10:04:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:04:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:04:01: 9000000 INFO @ Wed, 22 Apr 2020 10:04:02: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:04:02: 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 10:04:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.10_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/SRX7409540/SRX7409540.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:04:06: 10000000 INFO @ Wed, 22 Apr 2020 10:04:10: 11000000 INFO @ Wed, 22 Apr 2020 10:04:14: 12000000 INFO @ Wed, 22 Apr 2020 10:04:18: 13000000 INFO @ Wed, 22 Apr 2020 10:04:22: 14000000 INFO @ Wed, 22 Apr 2020 10:04:26: 15000000 INFO @ Wed, 22 Apr 2020 10:04:30: 16000000 INFO @ Wed, 22 Apr 2020 10:04:31: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:04:31: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:04:31: #1 total tags in treatment: 7911301 INFO @ Wed, 22 Apr 2020 10:04:31: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:04:31: #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 10:04:32: #1 tags after filtering in treatment: 6386539 INFO @ Wed, 22 Apr 2020 10:04:32: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 10:04:32: #1 finished! INFO @ Wed, 22 Apr 2020 10:04:32: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:04:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:04:32: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:04:32: 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 10:04:32: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.20_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/SRX7409540/SRX7409540.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409540/SRX7409540.20_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。