Job ID = 5790651 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T19:59:13 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 ) 2020-04-21T20:01:22 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 ) 2020-04-21T20:01:22 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 : 28,946,634 reads read : 57,893,268 reads written : 28,946,634 reads 0-length : 28,946,634 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 03:20:28 28946634 reads; of these: 28946634 (100.00%) were unpaired; of these: 14908044 (51.50%) aligned 0 times 5029559 (17.38%) aligned exactly 1 time 9009031 (31.12%) aligned >1 times 48.50% overall alignment rate Time searching: 03:20:30 Overall time: 03:20:30 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 8 files... [bam_rmdupse_core] 2324794 / 14038590 = 0.1656 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 08:44:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.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 08:44:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:44:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:44:27: 1000000 INFO @ Wed, 22 Apr 2020 08:44:34: 2000000 INFO @ Wed, 22 Apr 2020 08:44:41: 3000000 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 08:44:48: 4000000 INFO @ Wed, 22 Apr 2020 08:44:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.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 08:44:51: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:44:51: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:44:56: 5000000 INFO @ Wed, 22 Apr 2020 08:45:02: 1000000 INFO @ Wed, 22 Apr 2020 08:45:03: 6000000 INFO @ Wed, 22 Apr 2020 08:45:11: 7000000 INFO @ Wed, 22 Apr 2020 08:45:11: 2000000 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 08:45:19: 8000000 INFO @ Wed, 22 Apr 2020 08:45:20: 3000000 INFO @ Wed, 22 Apr 2020 08:45:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.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 08:45:22: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:45:22: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:45:27: 9000000 INFO @ Wed, 22 Apr 2020 08:45:29: 4000000 INFO @ Wed, 22 Apr 2020 08:45:30: 1000000 INFO @ Wed, 22 Apr 2020 08:45:35: 10000000 INFO @ Wed, 22 Apr 2020 08:45:38: 5000000 INFO @ Wed, 22 Apr 2020 08:45:38: 2000000 INFO @ Wed, 22 Apr 2020 08:45:42: 11000000 INFO @ Wed, 22 Apr 2020 08:45:46: 3000000 INFO @ Wed, 22 Apr 2020 08:45:47: 6000000 INFO @ Wed, 22 Apr 2020 08:45:48: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 08:45:48: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 08:45:48: #1 total tags in treatment: 11713796 INFO @ Wed, 22 Apr 2020 08:45:48: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:45:48: #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 08:45:48: #1 tags after filtering in treatment: 11713624 INFO @ Wed, 22 Apr 2020 08:45:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:45:48: #1 finished! INFO @ Wed, 22 Apr 2020 08:45:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:45:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:45:52: #2 number of paired peaks: 120195 INFO @ Wed, 22 Apr 2020 08:45:52: start model_add_line... INFO @ Wed, 22 Apr 2020 08:45:52: start X-correlation... INFO @ Wed, 22 Apr 2020 08:45:52: end of X-cor INFO @ Wed, 22 Apr 2020 08:45:52: #2 finished! INFO @ Wed, 22 Apr 2020 08:45:52: #2 predicted fragment length is 108 bps INFO @ Wed, 22 Apr 2020 08:45:52: #2 alternative fragment length(s) may be 108 bps INFO @ Wed, 22 Apr 2020 08:45:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.05_model.r WARNING @ Wed, 22 Apr 2020 08:45:52: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:45:52: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Wed, 22 Apr 2020 08:45:52: #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 08:45:52: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:45:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:45:53: 4000000 INFO @ Wed, 22 Apr 2020 08:45:55: 7000000 INFO @ Wed, 22 Apr 2020 08:46:01: 5000000 INFO @ Wed, 22 Apr 2020 08:46:04: 8000000 INFO @ Wed, 22 Apr 2020 08:46:09: 6000000 INFO @ Wed, 22 Apr 2020 08:46:14: 9000000 INFO @ Wed, 22 Apr 2020 08:46:17: 7000000 INFO @ Wed, 22 Apr 2020 08:46:20: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:46:23: 10000000 INFO @ Wed, 22 Apr 2020 08:46:25: 8000000 INFO @ Wed, 22 Apr 2020 08:46:32: 11000000 INFO @ Wed, 22 Apr 2020 08:46:32: 9000000 INFO @ Wed, 22 Apr 2020 08:46:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:46:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:46:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.05_summits.bed INFO @ Wed, 22 Apr 2020 08:46:35: Done! pass1 - making usageList (148 chroms): 5 millis pass2 - checking and writing primary data (37467 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:46:39: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 08:46:39: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 08:46:39: #1 total tags in treatment: 11713796 INFO @ Wed, 22 Apr 2020 08:46:39: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:46:39: #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 08:46:39: #1 tags after filtering in treatment: 11713624 INFO @ Wed, 22 Apr 2020 08:46:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:46:39: #1 finished! INFO @ Wed, 22 Apr 2020 08:46:39: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:46:40: 10000000 INFO @ Wed, 22 Apr 2020 08:46:43: #2 number of paired peaks: 120195 INFO @ Wed, 22 Apr 2020 08:46:43: start model_add_line... INFO @ Wed, 22 Apr 2020 08:46:43: start X-correlation... INFO @ Wed, 22 Apr 2020 08:46:43: end of X-cor INFO @ Wed, 22 Apr 2020 08:46:43: #2 finished! INFO @ Wed, 22 Apr 2020 08:46:43: #2 predicted fragment length is 108 bps INFO @ Wed, 22 Apr 2020 08:46:43: #2 alternative fragment length(s) may be 108 bps INFO @ Wed, 22 Apr 2020 08:46:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.10_model.r WARNING @ Wed, 22 Apr 2020 08:46:43: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:46:43: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Wed, 22 Apr 2020 08:46:43: #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 08:46:43: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:46:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:46:48: 11000000 INFO @ Wed, 22 Apr 2020 08:46:53: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 08:46:53: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 08:46:53: #1 total tags in treatment: 11713796 INFO @ Wed, 22 Apr 2020 08:46:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:46:53: #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 08:46:53: #1 tags after filtering in treatment: 11713624 INFO @ Wed, 22 Apr 2020 08:46:53: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:46:53: #1 finished! INFO @ Wed, 22 Apr 2020 08:46:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:46:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:46:57: #2 number of paired peaks: 120195 INFO @ Wed, 22 Apr 2020 08:46:57: start model_add_line... INFO @ Wed, 22 Apr 2020 08:46:57: start X-correlation... INFO @ Wed, 22 Apr 2020 08:46:57: end of X-cor INFO @ Wed, 22 Apr 2020 08:46:57: #2 finished! INFO @ Wed, 22 Apr 2020 08:46:57: #2 predicted fragment length is 108 bps INFO @ Wed, 22 Apr 2020 08:46:57: #2 alternative fragment length(s) may be 108 bps INFO @ Wed, 22 Apr 2020 08:46:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.20_model.r WARNING @ Wed, 22 Apr 2020 08:46:57: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:46:57: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Wed, 22 Apr 2020 08:46:57: #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 08:46:57: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:46:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:47:12: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:47:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:47:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:47:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:47:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.10_summits.bed INFO @ Wed, 22 Apr 2020 08:47:28: Done! pass1 - making usageList (81 chroms): 2 millis pass2 - checking and writing primary data (7685 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:47:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:47:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:47:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299294/SRX5299294.20_summits.bed INFO @ Wed, 22 Apr 2020 08:47:39: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (974 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。