Job ID = 5790643 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T19:44:17 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 ) 2020-04-21T19:45:01 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 ) 2020-04-21T19:54:35 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 : 48,556,790 reads read : 97,113,580 reads written : 48,556,790 reads 0-length : 48,556,790 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:34:50 48556790 reads; of these: 48556790 (100.00%) were unpaired; of these: 6293151 (12.96%) aligned 0 times 38649611 (79.60%) aligned exactly 1 time 3614028 (7.44%) aligned >1 times 87.04% overall alignment rate Time searching: 00:34:51 Overall time: 00:34:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 21996709 / 42263639 = 0.5205 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 05:57:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.bam'] # control file = None # effective genome size = 2.15e+09 # 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 05:57:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:57:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:57:30: 1000000 INFO @ Wed, 22 Apr 2020 05:57:36: 2000000 INFO @ Wed, 22 Apr 2020 05:57:42: 3000000 INFO @ Wed, 22 Apr 2020 05:57:49: 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 05:57:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.bam'] # control file = None # effective genome size = 2.15e+09 # 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 05:57:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:57:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:57:55: 5000000 INFO @ Wed, 22 Apr 2020 05:58:02: 1000000 INFO @ Wed, 22 Apr 2020 05:58:03: 6000000 INFO @ Wed, 22 Apr 2020 05:58:10: 7000000 INFO @ Wed, 22 Apr 2020 05:58:10: 2000000 INFO @ Wed, 22 Apr 2020 05:58:18: 8000000 INFO @ Wed, 22 Apr 2020 05:58:19: 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 05:58:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.bam'] # control file = None # effective genome size = 2.15e+09 # 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 05:58:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:58:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:58:25: 9000000 INFO @ Wed, 22 Apr 2020 05:58:27: 4000000 INFO @ Wed, 22 Apr 2020 05:58:32: 1000000 INFO @ Wed, 22 Apr 2020 05:58:33: 10000000 INFO @ Wed, 22 Apr 2020 05:58:35: 5000000 INFO @ Wed, 22 Apr 2020 05:58:41: 11000000 INFO @ Wed, 22 Apr 2020 05:58:41: 2000000 INFO @ Wed, 22 Apr 2020 05:58:43: 6000000 INFO @ Wed, 22 Apr 2020 05:58:48: 12000000 INFO @ Wed, 22 Apr 2020 05:58:50: 3000000 INFO @ Wed, 22 Apr 2020 05:58:52: 7000000 INFO @ Wed, 22 Apr 2020 05:58:56: 13000000 INFO @ Wed, 22 Apr 2020 05:58:58: 4000000 INFO @ Wed, 22 Apr 2020 05:59:00: 8000000 INFO @ Wed, 22 Apr 2020 05:59:03: 14000000 INFO @ Wed, 22 Apr 2020 05:59:07: 5000000 INFO @ Wed, 22 Apr 2020 05:59:08: 9000000 INFO @ Wed, 22 Apr 2020 05:59:11: 15000000 INFO @ Wed, 22 Apr 2020 05:59:15: 6000000 INFO @ Wed, 22 Apr 2020 05:59:17: 10000000 INFO @ Wed, 22 Apr 2020 05:59:18: 16000000 INFO @ Wed, 22 Apr 2020 05:59:23: 7000000 INFO @ Wed, 22 Apr 2020 05:59:25: 11000000 INFO @ Wed, 22 Apr 2020 05:59:26: 17000000 INFO @ Wed, 22 Apr 2020 05:59:32: 8000000 INFO @ Wed, 22 Apr 2020 05:59:33: 12000000 INFO @ Wed, 22 Apr 2020 05:59:33: 18000000 INFO @ Wed, 22 Apr 2020 05:59:40: 9000000 INFO @ Wed, 22 Apr 2020 05:59:41: 13000000 INFO @ Wed, 22 Apr 2020 05:59:42: 19000000 INFO @ Wed, 22 Apr 2020 05:59:48: 10000000 INFO @ Wed, 22 Apr 2020 05:59:50: 14000000 INFO @ Wed, 22 Apr 2020 05:59:51: 20000000 INFO @ Wed, 22 Apr 2020 05:59:53: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:59:53: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:59:53: #1 total tags in treatment: 20266930 INFO @ Wed, 22 Apr 2020 05:59:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:59:53: #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 05:59:53: #1 tags after filtering in treatment: 20266660 INFO @ Wed, 22 Apr 2020 05:59:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:59:53: #1 finished! INFO @ Wed, 22 Apr 2020 05:59:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:59:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:59:56: #2 number of paired peaks: 19992 INFO @ Wed, 22 Apr 2020 05:59:56: start model_add_line... INFO @ Wed, 22 Apr 2020 05:59:56: start X-correlation... INFO @ Wed, 22 Apr 2020 05:59:56: end of X-cor INFO @ Wed, 22 Apr 2020 05:59:56: #2 finished! INFO @ Wed, 22 Apr 2020 05:59:56: #2 predicted fragment length is 174 bps INFO @ Wed, 22 Apr 2020 05:59:56: #2 alternative fragment length(s) may be 174 bps INFO @ Wed, 22 Apr 2020 05:59:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.05_model.r WARNING @ Wed, 22 Apr 2020 05:59:56: #2 Since the d (174) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:59:56: #2 You may need to consider one of the other alternative d(s): 174 WARNING @ Wed, 22 Apr 2020 05:59:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 05:59:56: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:59:56: 11000000 INFO @ Wed, 22 Apr 2020 05:59:58: 15000000 INFO @ Wed, 22 Apr 2020 06:00:04: 12000000 INFO @ Wed, 22 Apr 2020 06:00:06: 16000000 INFO @ Wed, 22 Apr 2020 06:00:13: 13000000 INFO @ Wed, 22 Apr 2020 06:00:14: 17000000 INFO @ Wed, 22 Apr 2020 06:00:21: 14000000 INFO @ Wed, 22 Apr 2020 06:00:22: 18000000 INFO @ Wed, 22 Apr 2020 06:00:29: 15000000 INFO @ Wed, 22 Apr 2020 06:00:30: 19000000 INFO @ Wed, 22 Apr 2020 06:00:37: 16000000 INFO @ Wed, 22 Apr 2020 06:00:38: 20000000 INFO @ Wed, 22 Apr 2020 06:00:40: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:00:41: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 06:00:41: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 06:00:41: #1 total tags in treatment: 20266930 INFO @ Wed, 22 Apr 2020 06:00:41: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:00:41: #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 06:00:41: #1 tags after filtering in treatment: 20266660 INFO @ Wed, 22 Apr 2020 06:00:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:00:41: #1 finished! INFO @ Wed, 22 Apr 2020 06:00:41: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:00:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:00:43: #2 number of paired peaks: 19992 INFO @ Wed, 22 Apr 2020 06:00:43: start model_add_line... INFO @ Wed, 22 Apr 2020 06:00:43: start X-correlation... INFO @ Wed, 22 Apr 2020 06:00:43: end of X-cor INFO @ Wed, 22 Apr 2020 06:00:43: #2 finished! INFO @ Wed, 22 Apr 2020 06:00:43: #2 predicted fragment length is 174 bps INFO @ Wed, 22 Apr 2020 06:00:43: #2 alternative fragment length(s) may be 174 bps INFO @ Wed, 22 Apr 2020 06:00:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.10_model.r WARNING @ Wed, 22 Apr 2020 06:00:43: #2 Since the d (174) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:00:43: #2 You may need to consider one of the other alternative d(s): 174 WARNING @ Wed, 22 Apr 2020 06:00:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 06:00:43: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:00:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:00:45: 17000000 INFO @ Wed, 22 Apr 2020 06:00:52: 18000000 INFO @ Wed, 22 Apr 2020 06:00:59: 19000000 INFO @ Wed, 22 Apr 2020 06:01:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:01:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:01:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.05_summits.bed INFO @ Wed, 22 Apr 2020 06:01:02: Done! pass1 - making usageList (127 chroms): 3 millis pass2 - checking and writing primary data (23879 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:01:07: 20000000 INFO @ Wed, 22 Apr 2020 06:01:09: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 06:01:09: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 06:01:09: #1 total tags in treatment: 20266930 INFO @ Wed, 22 Apr 2020 06:01:09: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:01:09: #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 06:01:09: #1 tags after filtering in treatment: 20266660 INFO @ Wed, 22 Apr 2020 06:01:09: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:01:09: #1 finished! INFO @ Wed, 22 Apr 2020 06:01:09: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:01:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:01:12: #2 number of paired peaks: 19992 INFO @ Wed, 22 Apr 2020 06:01:12: start model_add_line... INFO @ Wed, 22 Apr 2020 06:01:12: start X-correlation... INFO @ Wed, 22 Apr 2020 06:01:12: end of X-cor INFO @ Wed, 22 Apr 2020 06:01:12: #2 finished! INFO @ Wed, 22 Apr 2020 06:01:12: #2 predicted fragment length is 174 bps INFO @ Wed, 22 Apr 2020 06:01:12: #2 alternative fragment length(s) may be 174 bps INFO @ Wed, 22 Apr 2020 06:01:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.20_model.r WARNING @ Wed, 22 Apr 2020 06:01:12: #2 Since the d (174) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:01:12: #2 You may need to consider one of the other alternative d(s): 174 WARNING @ Wed, 22 Apr 2020 06:01:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 06:01:12: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:01:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:01:27: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 06:01:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:01:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:01:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.10_summits.bed INFO @ Wed, 22 Apr 2020 06:01:48: Done! pass1 - making usageList (115 chroms): 4 millis pass2 - checking and writing primary data (21554 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:01:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 06:02:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:02:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:02:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299286/SRX5299286.20_summits.bed INFO @ Wed, 22 Apr 2020 06:02:16: Done! pass1 - making usageList (108 chroms): 3 millis pass2 - checking and writing primary data (19417 records, 4 fields): 21 millis CompletedMACS2peakCalling