Job ID = 5790685 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T21:05:04 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 ) 2020-04-21T21:05:04 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 ) 2020-04-21T21:05:04 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 ) 2020-04-21T21:05:04 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 : 26,790,063 reads read : 26,790,063 reads written : 26,790,063 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:28 26790063 reads; of these: 26790063 (100.00%) were unpaired; of these: 4640840 (17.32%) aligned 0 times 11011004 (41.10%) aligned exactly 1 time 11138219 (41.58%) aligned >1 times 82.68% overall alignment rate Time searching: 00:09:29 Overall time: 00:09:29 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] 3313752 / 22149223 = 0.1496 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 06:23:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.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 06:23:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:23:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:23:24: 1000000 INFO @ Wed, 22 Apr 2020 06:23:29: 2000000 INFO @ Wed, 22 Apr 2020 06:23:34: 3000000 INFO @ Wed, 22 Apr 2020 06:23:39: 4000000 INFO @ Wed, 22 Apr 2020 06:23:45: 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 06:23:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.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 06:23:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:23:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:23:50: 6000000 INFO @ Wed, 22 Apr 2020 06:23:56: 1000000 INFO @ Wed, 22 Apr 2020 06:23:56: 7000000 INFO @ Wed, 22 Apr 2020 06:24:03: 8000000 INFO @ Wed, 22 Apr 2020 06:24:03: 2000000 INFO @ Wed, 22 Apr 2020 06:24:09: 9000000 INFO @ Wed, 22 Apr 2020 06:24:10: 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 06:24:15: 10000000 INFO @ Wed, 22 Apr 2020 06:24:17: 4000000 INFO @ Wed, 22 Apr 2020 06:24:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.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 06:24:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:24:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:24:22: 11000000 INFO @ Wed, 22 Apr 2020 06:24:24: 5000000 INFO @ Wed, 22 Apr 2020 06:24:26: 1000000 INFO @ Wed, 22 Apr 2020 06:24:28: 12000000 INFO @ Wed, 22 Apr 2020 06:24:30: 6000000 INFO @ Wed, 22 Apr 2020 06:24:33: 2000000 INFO @ Wed, 22 Apr 2020 06:24:34: 13000000 INFO @ Wed, 22 Apr 2020 06:24:37: 7000000 INFO @ Wed, 22 Apr 2020 06:24:39: 3000000 INFO @ Wed, 22 Apr 2020 06:24:41: 14000000 INFO @ Wed, 22 Apr 2020 06:24:44: 8000000 INFO @ Wed, 22 Apr 2020 06:24:46: 4000000 INFO @ Wed, 22 Apr 2020 06:24:47: 15000000 INFO @ Wed, 22 Apr 2020 06:24:51: 9000000 INFO @ Wed, 22 Apr 2020 06:24:52: 5000000 INFO @ Wed, 22 Apr 2020 06:24:54: 16000000 INFO @ Wed, 22 Apr 2020 06:24:58: 10000000 INFO @ Wed, 22 Apr 2020 06:24:58: 6000000 INFO @ Wed, 22 Apr 2020 06:25:00: 17000000 INFO @ Wed, 22 Apr 2020 06:25:05: 7000000 INFO @ Wed, 22 Apr 2020 06:25:05: 11000000 INFO @ Wed, 22 Apr 2020 06:25:07: 18000000 INFO @ Wed, 22 Apr 2020 06:25:11: 8000000 INFO @ Wed, 22 Apr 2020 06:25:12: 12000000 INFO @ Wed, 22 Apr 2020 06:25:12: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:25:12: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:25:12: #1 total tags in treatment: 18835471 INFO @ Wed, 22 Apr 2020 06:25:12: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:25:12: #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 06:25:12: #1 tags after filtering in treatment: 18835364 INFO @ Wed, 22 Apr 2020 06:25:12: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:25:12: #1 finished! INFO @ Wed, 22 Apr 2020 06:25:12: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:25:14: #2 number of paired peaks: 11931 INFO @ Wed, 22 Apr 2020 06:25:14: start model_add_line... INFO @ Wed, 22 Apr 2020 06:25:15: start X-correlation... INFO @ Wed, 22 Apr 2020 06:25:15: end of X-cor INFO @ Wed, 22 Apr 2020 06:25:15: #2 finished! INFO @ Wed, 22 Apr 2020 06:25:15: #2 predicted fragment length is 38 bps INFO @ Wed, 22 Apr 2020 06:25:15: #2 alternative fragment length(s) may be 38,127 bps INFO @ Wed, 22 Apr 2020 06:25:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.05_model.r WARNING @ Wed, 22 Apr 2020 06:25:15: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:25:15: #2 You may need to consider one of the other alternative d(s): 38,127 WARNING @ Wed, 22 Apr 2020 06:25:15: #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 06:25:15: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:25:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:25:18: 9000000 INFO @ Wed, 22 Apr 2020 06:25:19: 13000000 INFO @ Wed, 22 Apr 2020 06:25:24: 10000000 INFO @ Wed, 22 Apr 2020 06:25:25: 14000000 INFO @ Wed, 22 Apr 2020 06:25:30: 11000000 INFO @ Wed, 22 Apr 2020 06:25:32: 15000000 INFO @ Wed, 22 Apr 2020 06:25:37: 12000000 INFO @ Wed, 22 Apr 2020 06:25:39: 16000000 INFO @ Wed, 22 Apr 2020 06:25:43: 13000000 INFO @ Wed, 22 Apr 2020 06:25:46: 17000000 INFO @ Wed, 22 Apr 2020 06:25:50: 14000000 INFO @ Wed, 22 Apr 2020 06:25:53: 18000000 INFO @ Wed, 22 Apr 2020 06:25:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:25:56: 15000000 INFO @ Wed, 22 Apr 2020 06:25:59: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:25:59: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:25:59: #1 total tags in treatment: 18835471 INFO @ Wed, 22 Apr 2020 06:25:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:25:59: #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 06:25:59: #1 tags after filtering in treatment: 18835364 INFO @ Wed, 22 Apr 2020 06:25:59: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:25:59: #1 finished! INFO @ Wed, 22 Apr 2020 06:25:59: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:25:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:26:01: #2 number of paired peaks: 11931 INFO @ Wed, 22 Apr 2020 06:26:01: start model_add_line... INFO @ Wed, 22 Apr 2020 06:26:01: start X-correlation... INFO @ Wed, 22 Apr 2020 06:26:01: end of X-cor INFO @ Wed, 22 Apr 2020 06:26:01: #2 finished! INFO @ Wed, 22 Apr 2020 06:26:01: #2 predicted fragment length is 38 bps INFO @ Wed, 22 Apr 2020 06:26:01: #2 alternative fragment length(s) may be 38,127 bps INFO @ Wed, 22 Apr 2020 06:26:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.10_model.r WARNING @ Wed, 22 Apr 2020 06:26:01: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:26:01: #2 You may need to consider one of the other alternative d(s): 38,127 WARNING @ Wed, 22 Apr 2020 06:26:01: #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 06:26:01: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:26:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:26:02: 16000000 INFO @ Wed, 22 Apr 2020 06:26:08: 17000000 INFO @ Wed, 22 Apr 2020 06:26:13: 18000000 INFO @ Wed, 22 Apr 2020 06:26:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:26:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:26:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.05_summits.bed INFO @ Wed, 22 Apr 2020 06:26:16: Done! INFO @ Wed, 22 Apr 2020 06:26:18: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 06:26:18: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 06:26:18: #1 total tags in treatment: 18835471 INFO @ Wed, 22 Apr 2020 06:26:18: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:26:18: #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 06:26:18: #1 tags after filtering in treatment: 18835364 INFO @ Wed, 22 Apr 2020 06:26:18: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:26:18: #1 finished! INFO @ Wed, 22 Apr 2020 06:26:18: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:26:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:26:20: #2 number of paired peaks: 11931 INFO @ Wed, 22 Apr 2020 06:26:20: start model_add_line... pass1 - making usageList (71 chroms): 1 millis pass2 - checking and writing primary data (3641 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:26:21: start X-correlation... INFO @ Wed, 22 Apr 2020 06:26:21: end of X-cor INFO @ Wed, 22 Apr 2020 06:26:21: #2 finished! INFO @ Wed, 22 Apr 2020 06:26:21: #2 predicted fragment length is 38 bps INFO @ Wed, 22 Apr 2020 06:26:21: #2 alternative fragment length(s) may be 38,127 bps INFO @ Wed, 22 Apr 2020 06:26:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.20_model.r WARNING @ Wed, 22 Apr 2020 06:26:21: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:26:21: #2 You may need to consider one of the other alternative d(s): 38,127 WARNING @ Wed, 22 Apr 2020 06:26:21: #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 06:26:21: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:26:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:26:41: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:27:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:27:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:27:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.10_summits.bed INFO @ Wed, 22 Apr 2020 06:27:01: Done! INFO @ Wed, 22 Apr 2020 06:27:02: #3 Call peaks for each chromosome... pass1 - making usageList (52 chroms): 0 millis pass2 - checking and writing primary data (1572 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 06:27:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:27:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:27:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5761717/SRX5761717.20_summits.bed INFO @ Wed, 22 Apr 2020 06:27:22: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (669 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。