Job ID = 5790646 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T19:51:13 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 ) 2020-04-21T19:55:01 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 ) spots read : 34,390,362 reads read : 68,780,724 reads written : 34,390,362 reads 0-length : 34,390,362 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 03:08:29 34390362 reads; of these: 34390362 (100.00%) were unpaired; of these: 18360836 (53.39%) aligned 0 times 5970961 (17.36%) aligned exactly 1 time 10058565 (29.25%) aligned >1 times 46.61% overall alignment rate Time searching: 03:08:32 Overall time: 03:08:32 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] 2762169 / 16029526 = 0.1723 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 08:25:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.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 08:25:06: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:25:06: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:25:16: 1000000 INFO @ Wed, 22 Apr 2020 08:25:26: 2000000 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 08:25:35: 3000000 INFO @ Wed, 22 Apr 2020 08:25:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.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 08:25:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:25:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:25:46: 4000000 INFO @ Wed, 22 Apr 2020 08:25:46: 1000000 INFO @ Wed, 22 Apr 2020 08:25:56: 2000000 INFO @ Wed, 22 Apr 2020 08:25:57: 5000000 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 08:26:05: 3000000 INFO @ Wed, 22 Apr 2020 08:26:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.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 08:26:06: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:26:06: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:26:08: 6000000 INFO @ Wed, 22 Apr 2020 08:26:15: 4000000 INFO @ Wed, 22 Apr 2020 08:26:17: 1000000 INFO @ Wed, 22 Apr 2020 08:26:19: 7000000 INFO @ Wed, 22 Apr 2020 08:26:26: 5000000 INFO @ Wed, 22 Apr 2020 08:26:28: 2000000 INFO @ Wed, 22 Apr 2020 08:26:30: 8000000 INFO @ Wed, 22 Apr 2020 08:26:36: 6000000 INFO @ Wed, 22 Apr 2020 08:26:39: 3000000 INFO @ Wed, 22 Apr 2020 08:26:41: 9000000 INFO @ Wed, 22 Apr 2020 08:26:46: 7000000 INFO @ Wed, 22 Apr 2020 08:26:50: 4000000 INFO @ Wed, 22 Apr 2020 08:26:53: 10000000 INFO @ Wed, 22 Apr 2020 08:26:56: 8000000 INFO @ Wed, 22 Apr 2020 08:27:02: 5000000 INFO @ Wed, 22 Apr 2020 08:27:04: 11000000 INFO @ Wed, 22 Apr 2020 08:27:06: 9000000 INFO @ Wed, 22 Apr 2020 08:27:13: 6000000 INFO @ Wed, 22 Apr 2020 08:27:15: 12000000 INFO @ Wed, 22 Apr 2020 08:27:16: 10000000 INFO @ Wed, 22 Apr 2020 08:27:24: 7000000 INFO @ Wed, 22 Apr 2020 08:27:26: 11000000 INFO @ Wed, 22 Apr 2020 08:27:26: 13000000 INFO @ Wed, 22 Apr 2020 08:27:29: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 08:27:29: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 08:27:29: #1 total tags in treatment: 13267357 INFO @ Wed, 22 Apr 2020 08:27:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:27:29: #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 08:27:29: #1 tags after filtering in treatment: 13267198 INFO @ Wed, 22 Apr 2020 08:27:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:27:29: #1 finished! INFO @ Wed, 22 Apr 2020 08:27:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:27:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:27:33: #2 number of paired peaks: 120307 INFO @ Wed, 22 Apr 2020 08:27:33: start model_add_line... INFO @ Wed, 22 Apr 2020 08:27:33: start X-correlation... INFO @ Wed, 22 Apr 2020 08:27:33: end of X-cor INFO @ Wed, 22 Apr 2020 08:27:33: #2 finished! INFO @ Wed, 22 Apr 2020 08:27:33: #2 predicted fragment length is 106 bps INFO @ Wed, 22 Apr 2020 08:27:33: #2 alternative fragment length(s) may be 106 bps INFO @ Wed, 22 Apr 2020 08:27:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.05_model.r WARNING @ Wed, 22 Apr 2020 08:27:33: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:27:33: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Wed, 22 Apr 2020 08:27:33: #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 08:27:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:27:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:27:35: 8000000 INFO @ Wed, 22 Apr 2020 08:27:36: 12000000 INFO @ Wed, 22 Apr 2020 08:27:46: 9000000 INFO @ Wed, 22 Apr 2020 08:27:46: 13000000 INFO @ Wed, 22 Apr 2020 08:27:49: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 08:27:49: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 08:27:49: #1 total tags in treatment: 13267357 INFO @ Wed, 22 Apr 2020 08:27:49: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:27:49: #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 08:27:49: #1 tags after filtering in treatment: 13267198 INFO @ Wed, 22 Apr 2020 08:27:49: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:27:49: #1 finished! INFO @ Wed, 22 Apr 2020 08:27:49: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:27:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:27:53: #2 number of paired peaks: 120307 INFO @ Wed, 22 Apr 2020 08:27:53: start model_add_line... INFO @ Wed, 22 Apr 2020 08:27:53: start X-correlation... INFO @ Wed, 22 Apr 2020 08:27:53: end of X-cor INFO @ Wed, 22 Apr 2020 08:27:53: #2 finished! INFO @ Wed, 22 Apr 2020 08:27:53: #2 predicted fragment length is 106 bps INFO @ Wed, 22 Apr 2020 08:27:53: #2 alternative fragment length(s) may be 106 bps INFO @ Wed, 22 Apr 2020 08:27:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.10_model.r WARNING @ Wed, 22 Apr 2020 08:27:53: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:27:53: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Wed, 22 Apr 2020 08:27:53: #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 08:27:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:27:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:27:56: 10000000 INFO @ Wed, 22 Apr 2020 08:28:03: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:28:06: 11000000 INFO @ Wed, 22 Apr 2020 08:28:16: 12000000 INFO @ Wed, 22 Apr 2020 08:28:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:28:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:28:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.05_summits.bed INFO @ Wed, 22 Apr 2020 08:28:20: Done! pass1 - making usageList (164 chroms): 6 millis pass2 - checking and writing primary data (45594 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:28:24: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:28:26: 13000000 INFO @ Wed, 22 Apr 2020 08:28:28: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 08:28:28: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 08:28:28: #1 total tags in treatment: 13267357 INFO @ Wed, 22 Apr 2020 08:28:28: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:28:28: #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 08:28:29: #1 tags after filtering in treatment: 13267198 INFO @ Wed, 22 Apr 2020 08:28:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:28:29: #1 finished! INFO @ Wed, 22 Apr 2020 08:28:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:28:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:28:32: #2 number of paired peaks: 120307 INFO @ Wed, 22 Apr 2020 08:28:32: start model_add_line... INFO @ Wed, 22 Apr 2020 08:28:33: start X-correlation... INFO @ Wed, 22 Apr 2020 08:28:33: end of X-cor INFO @ Wed, 22 Apr 2020 08:28:33: #2 finished! INFO @ Wed, 22 Apr 2020 08:28:33: #2 predicted fragment length is 106 bps INFO @ Wed, 22 Apr 2020 08:28:33: #2 alternative fragment length(s) may be 106 bps INFO @ Wed, 22 Apr 2020 08:28:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.20_model.r WARNING @ Wed, 22 Apr 2020 08:28:33: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:28:33: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Wed, 22 Apr 2020 08:28:33: #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 08:28:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:28:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:28:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:28:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:28:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.10_summits.bed INFO @ Wed, 22 Apr 2020 08:28:40: Done! pass1 - making usageList (97 chroms): 2 millis pass2 - checking and writing primary data (10988 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:29:02: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:29:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:29:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:29:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299289/SRX5299289.20_summits.bed INFO @ Wed, 22 Apr 2020 08:29:17: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1280 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。