Job ID = 5720852 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T17:12:28 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 ) 2020-04-15T17:12:28 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 ) 2020-04-15T17:12:28 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 ) 2020-04-15T17:12:28 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 ) 2020-04-15T17:16:56 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 ) 2020-04-15T17:16:57 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 : 32,183,063 reads read : 32,183,063 reads written : 32,183,063 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: 00:09:45 32183063 reads; of these: 32183063 (100.00%) were unpaired; of these: 1128796 (3.51%) aligned 0 times 22722104 (70.60%) aligned exactly 1 time 8332163 (25.89%) aligned >1 times 96.49% overall alignment rate Time searching: 00:09:45 Overall time: 00:09:45 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] 11584656 / 31054267 = 0.3730 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 02:36:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.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 02:36:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:36:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:36:36: 1000000 INFO @ Thu, 16 Apr 2020 02:36:41: 2000000 INFO @ Thu, 16 Apr 2020 02:36:46: 3000000 INFO @ Thu, 16 Apr 2020 02:36:51: 4000000 INFO @ Thu, 16 Apr 2020 02:36:56: 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 02:37:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.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 02:37:02: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:37:02: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:37:02: 6000000 INFO @ Thu, 16 Apr 2020 02:37:08: 1000000 INFO @ Thu, 16 Apr 2020 02:37:09: 7000000 INFO @ Thu, 16 Apr 2020 02:37:15: 8000000 INFO @ Thu, 16 Apr 2020 02:37:15: 2000000 INFO @ Thu, 16 Apr 2020 02:37:21: 9000000 INFO @ Thu, 16 Apr 2020 02:37:22: 3000000 INFO @ Thu, 16 Apr 2020 02:37:27: 10000000 INFO @ Thu, 16 Apr 2020 02:37:29: 4000000 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 02:37:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.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 02:37:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:37:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:37:33: 11000000 INFO @ Thu, 16 Apr 2020 02:37:35: 5000000 INFO @ Thu, 16 Apr 2020 02:37:37: 1000000 INFO @ Thu, 16 Apr 2020 02:37:39: 12000000 INFO @ Thu, 16 Apr 2020 02:37:42: 6000000 INFO @ Thu, 16 Apr 2020 02:37:44: 2000000 INFO @ Thu, 16 Apr 2020 02:37:45: 13000000 INFO @ Thu, 16 Apr 2020 02:37:49: 7000000 INFO @ Thu, 16 Apr 2020 02:37:51: 14000000 INFO @ Thu, 16 Apr 2020 02:37:51: 3000000 INFO @ Thu, 16 Apr 2020 02:37:56: 8000000 INFO @ Thu, 16 Apr 2020 02:37:57: 15000000 INFO @ Thu, 16 Apr 2020 02:37:58: 4000000 INFO @ Thu, 16 Apr 2020 02:38:03: 9000000 INFO @ Thu, 16 Apr 2020 02:38:03: 16000000 INFO @ Thu, 16 Apr 2020 02:38:05: 5000000 INFO @ Thu, 16 Apr 2020 02:38:09: 17000000 INFO @ Thu, 16 Apr 2020 02:38:09: 10000000 INFO @ Thu, 16 Apr 2020 02:38:12: 6000000 INFO @ Thu, 16 Apr 2020 02:38:15: 18000000 INFO @ Thu, 16 Apr 2020 02:38:16: 11000000 INFO @ Thu, 16 Apr 2020 02:38:18: 7000000 INFO @ Thu, 16 Apr 2020 02:38:21: 19000000 INFO @ Thu, 16 Apr 2020 02:38:23: 12000000 INFO @ Thu, 16 Apr 2020 02:38:24: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:38:24: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:38:24: #1 total tags in treatment: 19469611 INFO @ Thu, 16 Apr 2020 02:38:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:38:24: #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 02:38:24: #1 tags after filtering in treatment: 19469611 INFO @ Thu, 16 Apr 2020 02:38:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:38:24: #1 finished! INFO @ Thu, 16 Apr 2020 02:38:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:38:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:38:25: 8000000 INFO @ Thu, 16 Apr 2020 02:38:26: #2 number of paired peaks: 5569 INFO @ Thu, 16 Apr 2020 02:38:26: start model_add_line... INFO @ Thu, 16 Apr 2020 02:38:26: start X-correlation... INFO @ Thu, 16 Apr 2020 02:38:26: end of X-cor INFO @ Thu, 16 Apr 2020 02:38:26: #2 finished! INFO @ Thu, 16 Apr 2020 02:38:26: #2 predicted fragment length is 245 bps INFO @ Thu, 16 Apr 2020 02:38:26: #2 alternative fragment length(s) may be 245 bps INFO @ Thu, 16 Apr 2020 02:38:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.05_model.r INFO @ Thu, 16 Apr 2020 02:38:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:38:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:38:29: 13000000 INFO @ Thu, 16 Apr 2020 02:38:32: 9000000 INFO @ Thu, 16 Apr 2020 02:38:36: 14000000 INFO @ Thu, 16 Apr 2020 02:38:39: 10000000 INFO @ Thu, 16 Apr 2020 02:38:43: 15000000 INFO @ Thu, 16 Apr 2020 02:38:46: 11000000 INFO @ Thu, 16 Apr 2020 02:38:50: 16000000 INFO @ Thu, 16 Apr 2020 02:38:52: 12000000 INFO @ Thu, 16 Apr 2020 02:38:56: 17000000 INFO @ Thu, 16 Apr 2020 02:38:59: 13000000 INFO @ Thu, 16 Apr 2020 02:39:03: 18000000 INFO @ Thu, 16 Apr 2020 02:39:05: 14000000 INFO @ Thu, 16 Apr 2020 02:39:10: 19000000 INFO @ Thu, 16 Apr 2020 02:39:12: 15000000 INFO @ Thu, 16 Apr 2020 02:39:13: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:39:13: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:39:13: #1 total tags in treatment: 19469611 INFO @ Thu, 16 Apr 2020 02:39:13: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:39:13: #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 02:39:13: #1 tags after filtering in treatment: 19469611 INFO @ Thu, 16 Apr 2020 02:39:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:39:13: #1 finished! INFO @ Thu, 16 Apr 2020 02:39:13: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:39:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:39:15: #2 number of paired peaks: 5569 INFO @ Thu, 16 Apr 2020 02:39:15: start model_add_line... INFO @ Thu, 16 Apr 2020 02:39:15: start X-correlation... INFO @ Thu, 16 Apr 2020 02:39:15: end of X-cor INFO @ Thu, 16 Apr 2020 02:39:15: #2 finished! INFO @ Thu, 16 Apr 2020 02:39:15: #2 predicted fragment length is 245 bps INFO @ Thu, 16 Apr 2020 02:39:15: #2 alternative fragment length(s) may be 245 bps INFO @ Thu, 16 Apr 2020 02:39:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.10_model.r INFO @ Thu, 16 Apr 2020 02:39:15: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:39:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:39:18: 16000000 INFO @ Thu, 16 Apr 2020 02:39:25: 17000000 INFO @ Thu, 16 Apr 2020 02:39:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:39:31: 18000000 INFO @ Thu, 16 Apr 2020 02:39:37: 19000000 INFO @ Thu, 16 Apr 2020 02:39:40: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:39:40: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:39:40: #1 total tags in treatment: 19469611 INFO @ Thu, 16 Apr 2020 02:39:40: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:39:40: #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 02:39:41: #1 tags after filtering in treatment: 19469611 INFO @ Thu, 16 Apr 2020 02:39:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:39:41: #1 finished! INFO @ Thu, 16 Apr 2020 02:39:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:39:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:39:42: #2 number of paired peaks: 5569 INFO @ Thu, 16 Apr 2020 02:39:42: start model_add_line... INFO @ Thu, 16 Apr 2020 02:39:43: start X-correlation... INFO @ Thu, 16 Apr 2020 02:39:43: end of X-cor INFO @ Thu, 16 Apr 2020 02:39:43: #2 finished! INFO @ Thu, 16 Apr 2020 02:39:43: #2 predicted fragment length is 245 bps INFO @ Thu, 16 Apr 2020 02:39:43: #2 alternative fragment length(s) may be 245 bps INFO @ Thu, 16 Apr 2020 02:39:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.20_model.r INFO @ Thu, 16 Apr 2020 02:39:43: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:39:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:39:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:39:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:39:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.05_summits.bed INFO @ Thu, 16 Apr 2020 02:39:48: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10378 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:40:12: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:40:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:40:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.10_summits.bed INFO @ Thu, 16 Apr 2020 02:40:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8817 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 02:40:39: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:41:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:41:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:41:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436045/SRX5436045.20_summits.bed INFO @ Thu, 16 Apr 2020 02:41:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7026 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。