Job ID = 5790675 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T20:58:50 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 ) 2020-04-21T20:58:50 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 : 21,135,416 reads read : 21,135,416 reads written : 21,135,416 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: 00:09:12 21135416 reads; of these: 21135416 (100.00%) were unpaired; of these: 2151809 (10.18%) aligned 0 times 11165223 (52.83%) aligned exactly 1 time 7818384 (36.99%) aligned >1 times 89.82% overall alignment rate Time searching: 00:09:13 Overall time: 00:09:13 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] 1467137 / 18983607 = 0.0773 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 06:15:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.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 06:15:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:15:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:15:34: 1000000 INFO @ Wed, 22 Apr 2020 06:15:39: 2000000 INFO @ Wed, 22 Apr 2020 06:15:44: 3000000 INFO @ Wed, 22 Apr 2020 06:15:49: 4000000 INFO @ Wed, 22 Apr 2020 06:15:54: 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 @ Wed, 22 Apr 2020 06:15:59: 6000000 INFO @ Wed, 22 Apr 2020 06:15:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.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 06:15:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:15:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:16:04: 7000000 INFO @ Wed, 22 Apr 2020 06:16:04: 1000000 INFO @ Wed, 22 Apr 2020 06:16:09: 8000000 INFO @ Wed, 22 Apr 2020 06:16:09: 2000000 INFO @ Wed, 22 Apr 2020 06:16:14: 9000000 INFO @ Wed, 22 Apr 2020 06:16:14: 3000000 INFO @ Wed, 22 Apr 2020 06:16:19: 10000000 INFO @ Wed, 22 Apr 2020 06:16:20: 4000000 INFO @ Wed, 22 Apr 2020 06:16:24: 11000000 INFO @ Wed, 22 Apr 2020 06:16:25: 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 06:16:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.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 06:16:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:16:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:16:30: 12000000 INFO @ Wed, 22 Apr 2020 06:16:31: 6000000 INFO @ Wed, 22 Apr 2020 06:16:34: 1000000 INFO @ Wed, 22 Apr 2020 06:16:35: 13000000 INFO @ Wed, 22 Apr 2020 06:16:36: 7000000 INFO @ Wed, 22 Apr 2020 06:16:40: 2000000 INFO @ Wed, 22 Apr 2020 06:16:40: 14000000 INFO @ Wed, 22 Apr 2020 06:16:41: 8000000 INFO @ Wed, 22 Apr 2020 06:16:45: 3000000 INFO @ Wed, 22 Apr 2020 06:16:46: 15000000 INFO @ Wed, 22 Apr 2020 06:16:46: 9000000 INFO @ Wed, 22 Apr 2020 06:16:50: 4000000 INFO @ Wed, 22 Apr 2020 06:16:51: 16000000 INFO @ Wed, 22 Apr 2020 06:16:52: 10000000 INFO @ Wed, 22 Apr 2020 06:16:56: 5000000 INFO @ Wed, 22 Apr 2020 06:16:56: 17000000 INFO @ Wed, 22 Apr 2020 06:16:57: 11000000 INFO @ Wed, 22 Apr 2020 06:16:59: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:16:59: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:16:59: #1 total tags in treatment: 17516470 INFO @ Wed, 22 Apr 2020 06:16:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:16:59: #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 06:17:00: #1 tags after filtering in treatment: 17516331 INFO @ Wed, 22 Apr 2020 06:17:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:17:00: #1 finished! INFO @ Wed, 22 Apr 2020 06:17:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:17:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:17:01: 6000000 INFO @ Wed, 22 Apr 2020 06:17:01: #2 number of paired peaks: 5397 INFO @ Wed, 22 Apr 2020 06:17:01: start model_add_line... INFO @ Wed, 22 Apr 2020 06:17:01: start X-correlation... INFO @ Wed, 22 Apr 2020 06:17:01: end of X-cor INFO @ Wed, 22 Apr 2020 06:17:01: #2 finished! INFO @ Wed, 22 Apr 2020 06:17:01: #2 predicted fragment length is 36 bps INFO @ Wed, 22 Apr 2020 06:17:01: #2 alternative fragment length(s) may be 36,113,216,397,573,588 bps INFO @ Wed, 22 Apr 2020 06:17:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.05_model.r WARNING @ Wed, 22 Apr 2020 06:17:01: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:17:01: #2 You may need to consider one of the other alternative d(s): 36,113,216,397,573,588 WARNING @ Wed, 22 Apr 2020 06:17:01: #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 06:17:01: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:17:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:17:02: 12000000 INFO @ Wed, 22 Apr 2020 06:17:06: 7000000 INFO @ Wed, 22 Apr 2020 06:17:07: 13000000 INFO @ Wed, 22 Apr 2020 06:17:11: 8000000 INFO @ Wed, 22 Apr 2020 06:17:12: 14000000 INFO @ Wed, 22 Apr 2020 06:17:16: 9000000 INFO @ Wed, 22 Apr 2020 06:17:17: 15000000 INFO @ Wed, 22 Apr 2020 06:17:22: 10000000 INFO @ Wed, 22 Apr 2020 06:17:23: 16000000 INFO @ Wed, 22 Apr 2020 06:17:27: 11000000 INFO @ Wed, 22 Apr 2020 06:17:28: 17000000 INFO @ Wed, 22 Apr 2020 06:17:31: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:17:31: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:17:31: #1 total tags in treatment: 17516470 INFO @ Wed, 22 Apr 2020 06:17:31: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:17:31: #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 06:17:31: #1 tags after filtering in treatment: 17516331 INFO @ Wed, 22 Apr 2020 06:17:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:17:31: #1 finished! INFO @ Wed, 22 Apr 2020 06:17:31: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:17:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:17:32: 12000000 INFO @ Wed, 22 Apr 2020 06:17:33: #2 number of paired peaks: 5397 INFO @ Wed, 22 Apr 2020 06:17:33: start model_add_line... INFO @ Wed, 22 Apr 2020 06:17:33: start X-correlation... INFO @ Wed, 22 Apr 2020 06:17:33: end of X-cor INFO @ Wed, 22 Apr 2020 06:17:33: #2 finished! INFO @ Wed, 22 Apr 2020 06:17:33: #2 predicted fragment length is 36 bps INFO @ Wed, 22 Apr 2020 06:17:33: #2 alternative fragment length(s) may be 36,113,216,397,573,588 bps INFO @ Wed, 22 Apr 2020 06:17:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.10_model.r WARNING @ Wed, 22 Apr 2020 06:17:33: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:17:33: #2 You may need to consider one of the other alternative d(s): 36,113,216,397,573,588 WARNING @ Wed, 22 Apr 2020 06:17:33: #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 06:17:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:17:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:17:37: 13000000 INFO @ Wed, 22 Apr 2020 06:17:40: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:17:42: 14000000 INFO @ Wed, 22 Apr 2020 06:17:47: 15000000 INFO @ Wed, 22 Apr 2020 06:17:51: 16000000 INFO @ Wed, 22 Apr 2020 06:17:56: 17000000 INFO @ Wed, 22 Apr 2020 06:17:59: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:17:59: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:17:59: #1 total tags in treatment: 17516470 INFO @ Wed, 22 Apr 2020 06:17:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:17:59: #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 06:17:59: #1 tags after filtering in treatment: 17516331 INFO @ Wed, 22 Apr 2020 06:17:59: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:17:59: #1 finished! INFO @ Wed, 22 Apr 2020 06:17:59: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:17:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:18:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:18:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:18:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.05_summits.bed INFO @ Wed, 22 Apr 2020 06:18:00: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (1761 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:18:01: #2 number of paired peaks: 5397 INFO @ Wed, 22 Apr 2020 06:18:01: start model_add_line... INFO @ Wed, 22 Apr 2020 06:18:01: start X-correlation... INFO @ Wed, 22 Apr 2020 06:18:01: end of X-cor INFO @ Wed, 22 Apr 2020 06:18:01: #2 finished! INFO @ Wed, 22 Apr 2020 06:18:01: #2 predicted fragment length is 36 bps INFO @ Wed, 22 Apr 2020 06:18:01: #2 alternative fragment length(s) may be 36,113,216,397,573,588 bps INFO @ Wed, 22 Apr 2020 06:18:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.20_model.r WARNING @ Wed, 22 Apr 2020 06:18:01: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:18:01: #2 You may need to consider one of the other alternative d(s): 36,113,216,397,573,588 WARNING @ Wed, 22 Apr 2020 06:18:01: #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 06:18:01: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:18:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:18:11: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:18:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:18:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:18:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.10_summits.bed INFO @ Wed, 22 Apr 2020 06:18:31: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (996 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:18:40: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:18:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:18:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:18:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761710/SRX5761710.20_summits.bed INFO @ Wed, 22 Apr 2020 06:18:59: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (426 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。