Job ID = 5720960 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T18:30:29 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 ) 2020-04-15T18:30:29 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 ) 2020-04-15T18:30:43 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 ) 2020-04-15T18:30:43 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 ) 2020-04-15T18:32:13 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 : 27,925,816 reads read : 27,925,816 reads written : 27,925,816 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: 00:08:27 27925816 reads; of these: 27925816 (100.00%) were unpaired; of these: 3884558 (13.91%) aligned 0 times 17640731 (63.17%) aligned exactly 1 time 6400527 (22.92%) aligned >1 times 86.09% overall alignment rate Time searching: 00:08:27 Overall time: 00:08:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 9924091 / 24041258 = 0.4128 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 03:54:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.bam'] # control file = None # effective genome size = 1.20e+08 # 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 03:54:15: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:54:15: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:54:20: 1000000 INFO @ Thu, 16 Apr 2020 03:54:26: 2000000 INFO @ Thu, 16 Apr 2020 03:54:31: 3000000 INFO @ Thu, 16 Apr 2020 03:54:36: 4000000 INFO @ Thu, 16 Apr 2020 03:54:42: 5000000 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 03:54:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.bam'] # control file = None # effective genome size = 1.20e+08 # 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 03:54:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:54:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:54:47: 6000000 INFO @ Thu, 16 Apr 2020 03:54:50: 1000000 INFO @ Thu, 16 Apr 2020 03:54:53: 7000000 INFO @ Thu, 16 Apr 2020 03:54:56: 2000000 INFO @ Thu, 16 Apr 2020 03:54:59: 8000000 INFO @ Thu, 16 Apr 2020 03:55:02: 3000000 INFO @ Thu, 16 Apr 2020 03:55:05: 9000000 INFO @ Thu, 16 Apr 2020 03:55:08: 4000000 INFO @ Thu, 16 Apr 2020 03:55:11: 10000000 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 03:55:14: 5000000 INFO @ Thu, 16 Apr 2020 03:55:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.bam'] # control file = None # effective genome size = 1.20e+08 # 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 03:55:14: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:55:14: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:55:17: 11000000 INFO @ Thu, 16 Apr 2020 03:55:20: 6000000 INFO @ Thu, 16 Apr 2020 03:55:20: 1000000 INFO @ Thu, 16 Apr 2020 03:55:23: 12000000 INFO @ Thu, 16 Apr 2020 03:55:26: 7000000 INFO @ Thu, 16 Apr 2020 03:55:27: 2000000 INFO @ Thu, 16 Apr 2020 03:55:29: 13000000 INFO @ Thu, 16 Apr 2020 03:55:32: 8000000 INFO @ Thu, 16 Apr 2020 03:55:33: 3000000 INFO @ Thu, 16 Apr 2020 03:55:36: 14000000 INFO @ Thu, 16 Apr 2020 03:55:37: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:55:37: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:55:37: #1 total tags in treatment: 14117167 INFO @ Thu, 16 Apr 2020 03:55:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:55:37: #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 03:55:37: #1 tags after filtering in treatment: 14117167 INFO @ Thu, 16 Apr 2020 03:55:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:55:37: #1 finished! INFO @ Thu, 16 Apr 2020 03:55:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:55:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:55:38: #2 number of paired peaks: 285 WARNING @ Thu, 16 Apr 2020 03:55:38: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Thu, 16 Apr 2020 03:55:38: start model_add_line... INFO @ Thu, 16 Apr 2020 03:55:38: start X-correlation... INFO @ Thu, 16 Apr 2020 03:55:38: end of X-cor INFO @ Thu, 16 Apr 2020 03:55:38: #2 finished! INFO @ Thu, 16 Apr 2020 03:55:38: #2 predicted fragment length is 178 bps INFO @ Thu, 16 Apr 2020 03:55:38: #2 alternative fragment length(s) may be 178 bps INFO @ Thu, 16 Apr 2020 03:55:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.05_model.r INFO @ Thu, 16 Apr 2020 03:55:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:55:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:55:38: 9000000 INFO @ Thu, 16 Apr 2020 03:55:40: 4000000 INFO @ Thu, 16 Apr 2020 03:55:44: 10000000 INFO @ Thu, 16 Apr 2020 03:55:46: 5000000 INFO @ Thu, 16 Apr 2020 03:55:50: 11000000 INFO @ Thu, 16 Apr 2020 03:55:52: 6000000 INFO @ Thu, 16 Apr 2020 03:55:56: 12000000 INFO @ Thu, 16 Apr 2020 03:55:58: 7000000 INFO @ Thu, 16 Apr 2020 03:56:03: 13000000 INFO @ Thu, 16 Apr 2020 03:56:04: 8000000 INFO @ Thu, 16 Apr 2020 03:56:08: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:56:09: 14000000 INFO @ Thu, 16 Apr 2020 03:56:09: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:56:09: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:56:09: #1 total tags in treatment: 14117167 INFO @ Thu, 16 Apr 2020 03:56:09: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:56:09: #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 03:56:09: #1 tags after filtering in treatment: 14117167 INFO @ Thu, 16 Apr 2020 03:56:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:56:09: #1 finished! INFO @ Thu, 16 Apr 2020 03:56:09: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:56:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:56:10: 9000000 INFO @ Thu, 16 Apr 2020 03:56:10: #2 number of paired peaks: 285 WARNING @ Thu, 16 Apr 2020 03:56:10: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Thu, 16 Apr 2020 03:56:10: start model_add_line... INFO @ Thu, 16 Apr 2020 03:56:11: start X-correlation... INFO @ Thu, 16 Apr 2020 03:56:11: end of X-cor INFO @ Thu, 16 Apr 2020 03:56:11: #2 finished! INFO @ Thu, 16 Apr 2020 03:56:11: #2 predicted fragment length is 178 bps INFO @ Thu, 16 Apr 2020 03:56:11: #2 alternative fragment length(s) may be 178 bps INFO @ Thu, 16 Apr 2020 03:56:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.10_model.r INFO @ Thu, 16 Apr 2020 03:56:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:56:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:56:15: 10000000 INFO @ Thu, 16 Apr 2020 03:56:21: 11000000 INFO @ Thu, 16 Apr 2020 03:56:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:56:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:56:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.05_summits.bed INFO @ Thu, 16 Apr 2020 03:56:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4635 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:56:27: 12000000 INFO @ Thu, 16 Apr 2020 03:56:32: 13000000 INFO @ Thu, 16 Apr 2020 03:56:38: 14000000 INFO @ Thu, 16 Apr 2020 03:56:39: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:56:39: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:56:39: #1 total tags in treatment: 14117167 INFO @ Thu, 16 Apr 2020 03:56:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:56:39: #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 03:56:39: #1 tags after filtering in treatment: 14117167 INFO @ Thu, 16 Apr 2020 03:56:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:56:39: #1 finished! INFO @ Thu, 16 Apr 2020 03:56:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:56:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:56:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:56:40: #2 number of paired peaks: 285 WARNING @ Thu, 16 Apr 2020 03:56:40: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Thu, 16 Apr 2020 03:56:40: start model_add_line... INFO @ Thu, 16 Apr 2020 03:56:40: start X-correlation... INFO @ Thu, 16 Apr 2020 03:56:40: end of X-cor INFO @ Thu, 16 Apr 2020 03:56:40: #2 finished! INFO @ Thu, 16 Apr 2020 03:56:40: #2 predicted fragment length is 178 bps INFO @ Thu, 16 Apr 2020 03:56:40: #2 alternative fragment length(s) may be 178 bps INFO @ Thu, 16 Apr 2020 03:56:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.20_model.r INFO @ Thu, 16 Apr 2020 03:56:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:56:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:56:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:56:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:56:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.10_summits.bed INFO @ Thu, 16 Apr 2020 03:56:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2565 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:57:09: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:57:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:57:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:57:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386753/SRX6386753.20_summits.bed INFO @ Thu, 16 Apr 2020 03:57:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1355 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。