Job ID = 5790638 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T20:05:35 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 56,834,171 reads read : 113,668,342 reads written : 56,834,171 reads 0-length : 56,834,171 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: 00:39:24 56834171 reads; of these: 56834171 (100.00%) were unpaired; of these: 5563248 (9.79%) aligned 0 times 46883063 (82.49%) aligned exactly 1 time 4387860 (7.72%) aligned >1 times 90.21% overall alignment rate Time searching: 00:39:25 Overall time: 00:39:25 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 24 files... [bam_rmdupse_core] 29176287 / 51270923 = 0.5691 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 06:00:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.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 06:00:55: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:00:55: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:01:01: 1000000 INFO @ Wed, 22 Apr 2020 06:01:07: 2000000 INFO @ Wed, 22 Apr 2020 06:01:12: 3000000 INFO @ Wed, 22 Apr 2020 06:01:18: 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 06:01:24: 5000000 INFO @ Wed, 22 Apr 2020 06:01:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.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 06:01:25: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:01:25: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:01:31: 6000000 INFO @ Wed, 22 Apr 2020 06:01:32: 1000000 INFO @ Wed, 22 Apr 2020 06:01:37: 7000000 INFO @ Wed, 22 Apr 2020 06:01:39: 2000000 INFO @ Wed, 22 Apr 2020 06:01:44: 8000000 INFO @ Wed, 22 Apr 2020 06:01:45: 3000000 INFO @ Wed, 22 Apr 2020 06:01:50: 9000000 INFO @ Wed, 22 Apr 2020 06:01:52: 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 @ Wed, 22 Apr 2020 06:01:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.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 06:01:56: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:01:56: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:01:57: 10000000 INFO @ Wed, 22 Apr 2020 06:01:58: 5000000 INFO @ Wed, 22 Apr 2020 06:02:02: 1000000 INFO @ Wed, 22 Apr 2020 06:02:03: 11000000 INFO @ Wed, 22 Apr 2020 06:02:05: 6000000 INFO @ Wed, 22 Apr 2020 06:02:09: 2000000 INFO @ Wed, 22 Apr 2020 06:02:10: 12000000 INFO @ Wed, 22 Apr 2020 06:02:12: 7000000 INFO @ Wed, 22 Apr 2020 06:02:15: 3000000 INFO @ Wed, 22 Apr 2020 06:02:17: 13000000 INFO @ Wed, 22 Apr 2020 06:02:18: 8000000 INFO @ Wed, 22 Apr 2020 06:02:22: 4000000 INFO @ Wed, 22 Apr 2020 06:02:23: 14000000 INFO @ Wed, 22 Apr 2020 06:02:25: 9000000 INFO @ Wed, 22 Apr 2020 06:02:28: 5000000 INFO @ Wed, 22 Apr 2020 06:02:30: 15000000 INFO @ Wed, 22 Apr 2020 06:02:31: 10000000 INFO @ Wed, 22 Apr 2020 06:02:35: 6000000 INFO @ Wed, 22 Apr 2020 06:02:36: 16000000 INFO @ Wed, 22 Apr 2020 06:02:38: 11000000 INFO @ Wed, 22 Apr 2020 06:02:42: 7000000 INFO @ Wed, 22 Apr 2020 06:02:43: 17000000 INFO @ Wed, 22 Apr 2020 06:02:44: 12000000 INFO @ Wed, 22 Apr 2020 06:02:48: 8000000 INFO @ Wed, 22 Apr 2020 06:02:49: 18000000 INFO @ Wed, 22 Apr 2020 06:02:51: 13000000 INFO @ Wed, 22 Apr 2020 06:02:55: 9000000 INFO @ Wed, 22 Apr 2020 06:02:56: 19000000 INFO @ Wed, 22 Apr 2020 06:02:57: 14000000 INFO @ Wed, 22 Apr 2020 06:03:01: 10000000 INFO @ Wed, 22 Apr 2020 06:03:02: 20000000 INFO @ Wed, 22 Apr 2020 06:03:04: 15000000 INFO @ Wed, 22 Apr 2020 06:03:08: 11000000 INFO @ Wed, 22 Apr 2020 06:03:09: 21000000 INFO @ Wed, 22 Apr 2020 06:03:10: 16000000 INFO @ Wed, 22 Apr 2020 06:03:14: 12000000 INFO @ Wed, 22 Apr 2020 06:03:16: 22000000 INFO @ Wed, 22 Apr 2020 06:03:16: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 06:03:16: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 06:03:16: #1 total tags in treatment: 22094636 INFO @ Wed, 22 Apr 2020 06:03:16: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:03:16: #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 06:03:17: 17000000 INFO @ Wed, 22 Apr 2020 06:03:17: #1 tags after filtering in treatment: 22094412 INFO @ Wed, 22 Apr 2020 06:03:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:03:17: #1 finished! INFO @ Wed, 22 Apr 2020 06:03:17: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:03:19: #2 number of paired peaks: 19640 INFO @ Wed, 22 Apr 2020 06:03:19: start model_add_line... INFO @ Wed, 22 Apr 2020 06:03:19: start X-correlation... INFO @ Wed, 22 Apr 2020 06:03:19: end of X-cor INFO @ Wed, 22 Apr 2020 06:03:19: #2 finished! INFO @ Wed, 22 Apr 2020 06:03:19: #2 predicted fragment length is 185 bps INFO @ Wed, 22 Apr 2020 06:03:19: #2 alternative fragment length(s) may be 185 bps INFO @ Wed, 22 Apr 2020 06:03:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.05_model.r WARNING @ Wed, 22 Apr 2020 06:03:19: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:03:19: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Wed, 22 Apr 2020 06:03:19: #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 06:03:19: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:03:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:03:21: 13000000 INFO @ Wed, 22 Apr 2020 06:03:23: 18000000 INFO @ Wed, 22 Apr 2020 06:03:27: 14000000 INFO @ Wed, 22 Apr 2020 06:03:30: 19000000 INFO @ Wed, 22 Apr 2020 06:03:34: 15000000 INFO @ Wed, 22 Apr 2020 06:03:36: 20000000 INFO @ Wed, 22 Apr 2020 06:03:41: 16000000 INFO @ Wed, 22 Apr 2020 06:03:42: 21000000 INFO @ Wed, 22 Apr 2020 06:03:47: 17000000 INFO @ Wed, 22 Apr 2020 06:03:49: 22000000 INFO @ Wed, 22 Apr 2020 06:03:50: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 06:03:50: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 06:03:50: #1 total tags in treatment: 22094636 INFO @ Wed, 22 Apr 2020 06:03:50: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:03:50: #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 06:03:50: #1 tags after filtering in treatment: 22094412 INFO @ Wed, 22 Apr 2020 06:03:50: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:03:50: #1 finished! INFO @ Wed, 22 Apr 2020 06:03:50: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:03:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:03:53: #2 number of paired peaks: 19640 INFO @ Wed, 22 Apr 2020 06:03:53: start model_add_line... INFO @ Wed, 22 Apr 2020 06:03:53: start X-correlation... INFO @ Wed, 22 Apr 2020 06:03:53: end of X-cor INFO @ Wed, 22 Apr 2020 06:03:53: #2 finished! INFO @ Wed, 22 Apr 2020 06:03:53: #2 predicted fragment length is 185 bps INFO @ Wed, 22 Apr 2020 06:03:53: #2 alternative fragment length(s) may be 185 bps INFO @ Wed, 22 Apr 2020 06:03:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.10_model.r WARNING @ Wed, 22 Apr 2020 06:03:53: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:03:53: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Wed, 22 Apr 2020 06:03:53: #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 06:03:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:03:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:03:56: 18000000 INFO @ Wed, 22 Apr 2020 06:04:02: 19000000 INFO @ Wed, 22 Apr 2020 06:04:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:04:08: 20000000 INFO @ Wed, 22 Apr 2020 06:04:14: 21000000 INFO @ Wed, 22 Apr 2020 06:04:21: 22000000 INFO @ Wed, 22 Apr 2020 06:04:21: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 06:04:21: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 06:04:21: #1 total tags in treatment: 22094636 INFO @ Wed, 22 Apr 2020 06:04:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:04:21: #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 06:04:22: #1 tags after filtering in treatment: 22094412 INFO @ Wed, 22 Apr 2020 06:04:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:04:22: #1 finished! INFO @ Wed, 22 Apr 2020 06:04:22: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:04:24: #2 number of paired peaks: 19640 INFO @ Wed, 22 Apr 2020 06:04:24: start model_add_line... INFO @ Wed, 22 Apr 2020 06:04:24: start X-correlation... INFO @ Wed, 22 Apr 2020 06:04:24: end of X-cor INFO @ Wed, 22 Apr 2020 06:04:24: #2 finished! INFO @ Wed, 22 Apr 2020 06:04:24: #2 predicted fragment length is 185 bps INFO @ Wed, 22 Apr 2020 06:04:24: #2 alternative fragment length(s) may be 185 bps INFO @ Wed, 22 Apr 2020 06:04:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.20_model.r WARNING @ Wed, 22 Apr 2020 06:04:24: #2 Since the d (185) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:04:24: #2 You may need to consider one of the other alternative d(s): 185 WARNING @ Wed, 22 Apr 2020 06:04:24: #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 06:04:24: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:04:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:04:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:04:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:04:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.05_summits.bed INFO @ Wed, 22 Apr 2020 06:04:31: Done! pass1 - making usageList (134 chroms): 4 millis pass2 - checking and writing primary data (23693 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:04:41: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 06:05:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:05:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:05:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.10_summits.bed INFO @ Wed, 22 Apr 2020 06:05:04: Done! pass1 - making usageList (119 chroms): 3 millis pass2 - checking and writing primary data (21282 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 06:05:13: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:05:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:05:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:05:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299282/SRX5299282.20_summits.bed INFO @ Wed, 22 Apr 2020 06:05:35: Done! pass1 - making usageList (106 chroms): 4 millis pass2 - checking and writing primary data (19204 records, 4 fields): 20 millis CompletedMACS2peakCalling