Job ID = 5720848 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T17:12:59 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 ) 2020-04-15T17:12:59 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 : 34,934,147 reads read : 34,934,147 reads written : 34,934,147 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: 00:09:51 34934147 reads; of these: 34934147 (100.00%) were unpaired; of these: 921433 (2.64%) aligned 0 times 25563059 (73.17%) aligned exactly 1 time 8449655 (24.19%) aligned >1 times 97.36% overall alignment rate Time searching: 00:09:51 Overall time: 00:09:51 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 16 files... [bam_rmdupse_core] 14005804 / 34012714 = 0.4118 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 02:37:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.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 02:37:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:37:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:37:37: 1000000 INFO @ Thu, 16 Apr 2020 02:37:42: 2000000 INFO @ Thu, 16 Apr 2020 02:37:47: 3000000 INFO @ Thu, 16 Apr 2020 02:37:53: 4000000 INFO @ Thu, 16 Apr 2020 02:37:58: 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 02:38:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.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 02:38:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:38:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:38:04: 6000000 INFO @ Thu, 16 Apr 2020 02:38:08: 1000000 INFO @ Thu, 16 Apr 2020 02:38:10: 7000000 INFO @ Thu, 16 Apr 2020 02:38:14: 2000000 INFO @ Thu, 16 Apr 2020 02:38:16: 8000000 INFO @ Thu, 16 Apr 2020 02:38:20: 3000000 INFO @ Thu, 16 Apr 2020 02:38:23: 9000000 INFO @ Thu, 16 Apr 2020 02:38:26: 4000000 INFO @ Thu, 16 Apr 2020 02:38:29: 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 02:38:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.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 02:38:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:38:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:38:33: 5000000 INFO @ Thu, 16 Apr 2020 02:38:35: 11000000 INFO @ Thu, 16 Apr 2020 02:38:38: 1000000 INFO @ Thu, 16 Apr 2020 02:38:39: 6000000 INFO @ Thu, 16 Apr 2020 02:38:41: 12000000 INFO @ Thu, 16 Apr 2020 02:38:44: 2000000 INFO @ Thu, 16 Apr 2020 02:38:45: 7000000 INFO @ Thu, 16 Apr 2020 02:38:47: 13000000 INFO @ Thu, 16 Apr 2020 02:38:50: 3000000 INFO @ Thu, 16 Apr 2020 02:38:51: 8000000 INFO @ Thu, 16 Apr 2020 02:38:54: 14000000 INFO @ Thu, 16 Apr 2020 02:38:56: 4000000 INFO @ Thu, 16 Apr 2020 02:38:58: 9000000 INFO @ Thu, 16 Apr 2020 02:39:00: 15000000 INFO @ Thu, 16 Apr 2020 02:39:03: 5000000 INFO @ Thu, 16 Apr 2020 02:39:04: 10000000 INFO @ Thu, 16 Apr 2020 02:39:06: 16000000 INFO @ Thu, 16 Apr 2020 02:39:09: 6000000 INFO @ Thu, 16 Apr 2020 02:39:10: 11000000 INFO @ Thu, 16 Apr 2020 02:39:12: 17000000 INFO @ Thu, 16 Apr 2020 02:39:15: 7000000 INFO @ Thu, 16 Apr 2020 02:39:16: 12000000 INFO @ Thu, 16 Apr 2020 02:39:19: 18000000 INFO @ Thu, 16 Apr 2020 02:39:21: 8000000 INFO @ Thu, 16 Apr 2020 02:39:22: 13000000 INFO @ Thu, 16 Apr 2020 02:39:25: 19000000 INFO @ Thu, 16 Apr 2020 02:39:27: 9000000 INFO @ Thu, 16 Apr 2020 02:39:29: 14000000 INFO @ Thu, 16 Apr 2020 02:39:31: 20000000 INFO @ Thu, 16 Apr 2020 02:39:31: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:39:31: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:39:31: #1 total tags in treatment: 20006910 INFO @ Thu, 16 Apr 2020 02:39:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:39:31: #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 02:39:32: #1 tags after filtering in treatment: 20006910 INFO @ Thu, 16 Apr 2020 02:39:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:39:32: #1 finished! INFO @ Thu, 16 Apr 2020 02:39:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:39:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:39:33: #2 number of paired peaks: 6789 INFO @ Thu, 16 Apr 2020 02:39:33: start model_add_line... INFO @ Thu, 16 Apr 2020 02:39:34: 10000000 INFO @ Thu, 16 Apr 2020 02:39:34: start X-correlation... INFO @ Thu, 16 Apr 2020 02:39:34: end of X-cor INFO @ Thu, 16 Apr 2020 02:39:34: #2 finished! INFO @ Thu, 16 Apr 2020 02:39:34: #2 predicted fragment length is 245 bps INFO @ Thu, 16 Apr 2020 02:39:34: #2 alternative fragment length(s) may be 245 bps INFO @ Thu, 16 Apr 2020 02:39:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.05_model.r INFO @ Thu, 16 Apr 2020 02:39:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:39:35: 15000000 INFO @ Thu, 16 Apr 2020 02:39:40: 11000000 INFO @ Thu, 16 Apr 2020 02:39:41: 16000000 INFO @ Thu, 16 Apr 2020 02:39:46: 12000000 INFO @ Thu, 16 Apr 2020 02:39:48: 17000000 INFO @ Thu, 16 Apr 2020 02:39:52: 13000000 INFO @ Thu, 16 Apr 2020 02:39:54: 18000000 INFO @ Thu, 16 Apr 2020 02:39:58: 14000000 INFO @ Thu, 16 Apr 2020 02:40:00: 19000000 INFO @ Thu, 16 Apr 2020 02:40:04: 15000000 INFO @ Thu, 16 Apr 2020 02:40:06: 20000000 INFO @ Thu, 16 Apr 2020 02:40:06: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:40:06: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:40:06: #1 total tags in treatment: 20006910 INFO @ Thu, 16 Apr 2020 02:40:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:40:06: #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 02:40:06: #1 tags after filtering in treatment: 20006910 INFO @ Thu, 16 Apr 2020 02:40:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:40:06: #1 finished! INFO @ Thu, 16 Apr 2020 02:40:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:40:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:40:08: #2 number of paired peaks: 6789 INFO @ Thu, 16 Apr 2020 02:40:08: start model_add_line... INFO @ Thu, 16 Apr 2020 02:40:09: start X-correlation... INFO @ Thu, 16 Apr 2020 02:40:09: end of X-cor INFO @ Thu, 16 Apr 2020 02:40:09: #2 finished! INFO @ Thu, 16 Apr 2020 02:40:09: #2 predicted fragment length is 245 bps INFO @ Thu, 16 Apr 2020 02:40:09: #2 alternative fragment length(s) may be 245 bps INFO @ Thu, 16 Apr 2020 02:40:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.10_model.r INFO @ Thu, 16 Apr 2020 02:40:09: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:40:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:40:10: 16000000 INFO @ Thu, 16 Apr 2020 02:40:16: 17000000 INFO @ Thu, 16 Apr 2020 02:40:22: 18000000 INFO @ Thu, 16 Apr 2020 02:40:27: 19000000 INFO @ Thu, 16 Apr 2020 02:40:33: 20000000 INFO @ Thu, 16 Apr 2020 02:40:33: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:40:33: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:40:33: #1 total tags in treatment: 20006910 INFO @ Thu, 16 Apr 2020 02:40:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:40:33: #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 02:40:34: #1 tags after filtering in treatment: 20006910 INFO @ Thu, 16 Apr 2020 02:40:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:40:34: #1 finished! INFO @ Thu, 16 Apr 2020 02:40:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:40:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:40:35: #2 number of paired peaks: 6789 INFO @ Thu, 16 Apr 2020 02:40:35: start model_add_line... INFO @ Thu, 16 Apr 2020 02:40:36: start X-correlation... INFO @ Thu, 16 Apr 2020 02:40:36: end of X-cor INFO @ Thu, 16 Apr 2020 02:40:36: #2 finished! INFO @ Thu, 16 Apr 2020 02:40:36: #2 predicted fragment length is 245 bps INFO @ Thu, 16 Apr 2020 02:40:36: #2 alternative fragment length(s) may be 245 bps INFO @ Thu, 16 Apr 2020 02:40:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.20_model.r INFO @ Thu, 16 Apr 2020 02:40:36: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:40:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:40:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.05_summits.bed INFO @ Thu, 16 Apr 2020 02:40:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11198 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:41:13: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 02:41:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:41:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:41:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.10_summits.bed INFO @ Thu, 16 Apr 2020 02:41:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9649 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:41:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 16 Apr 2020 02:41:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:41:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:41:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436041/SRX5436041.20_summits.bed INFO @ Thu, 16 Apr 2020 02:41:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7722 records, 4 fields): 8 millis CompletedMACS2peakCalling