Job ID = 5790647 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T19:52:09 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 : 25,135,420 reads read : 50,270,840 reads written : 25,135,420 reads 0-length : 25,135,420 spots read : 24,548,954 reads read : 49,097,908 reads written : 24,548,954 reads 0-length : 24,548,954 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: 01:57:30 49684374 reads; of these: 49684374 (100.00%) were unpaired; of these: 18263484 (36.76%) aligned 0 times 23816546 (47.94%) aligned exactly 1 time 7604344 (15.31%) aligned >1 times 63.24% overall alignment rate Time searching: 01:57:31 Overall time: 01:57:31 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 16 files... [bam_rmdupse_core] 4095323 / 31420890 = 0.1303 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 07:37:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.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 07:37:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:37:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:37:15: 1000000 INFO @ Wed, 22 Apr 2020 07:37:23: 2000000 INFO @ Wed, 22 Apr 2020 07:37:31: 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 07:37:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.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 07:37:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:37:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:37:39: 4000000 INFO @ Wed, 22 Apr 2020 07:37:45: 1000000 INFO @ Wed, 22 Apr 2020 07:37:47: 5000000 INFO @ Wed, 22 Apr 2020 07:37:53: 2000000 INFO @ Wed, 22 Apr 2020 07:37:55: 6000000 INFO @ Wed, 22 Apr 2020 07:38:01: 3000000 INFO @ Wed, 22 Apr 2020 07:38:03: 7000000 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 07:38:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.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 07:38:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:38:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:38:09: 4000000 INFO @ Wed, 22 Apr 2020 07:38:11: 8000000 INFO @ Wed, 22 Apr 2020 07:38:15: 1000000 INFO @ Wed, 22 Apr 2020 07:38:17: 5000000 INFO @ Wed, 22 Apr 2020 07:38:19: 9000000 INFO @ Wed, 22 Apr 2020 07:38:24: 2000000 INFO @ Wed, 22 Apr 2020 07:38:26: 6000000 INFO @ Wed, 22 Apr 2020 07:38:28: 10000000 INFO @ Wed, 22 Apr 2020 07:38:32: 3000000 INFO @ Wed, 22 Apr 2020 07:38:34: 7000000 INFO @ Wed, 22 Apr 2020 07:38:36: 11000000 INFO @ Wed, 22 Apr 2020 07:38:41: 4000000 INFO @ Wed, 22 Apr 2020 07:38:43: 8000000 INFO @ Wed, 22 Apr 2020 07:38:44: 12000000 INFO @ Wed, 22 Apr 2020 07:38:50: 5000000 INFO @ Wed, 22 Apr 2020 07:38:52: 13000000 INFO @ Wed, 22 Apr 2020 07:38:52: 9000000 INFO @ Wed, 22 Apr 2020 07:38:59: 6000000 INFO @ Wed, 22 Apr 2020 07:39:00: 14000000 INFO @ Wed, 22 Apr 2020 07:39:01: 10000000 INFO @ Wed, 22 Apr 2020 07:39:08: 7000000 INFO @ Wed, 22 Apr 2020 07:39:08: 15000000 INFO @ Wed, 22 Apr 2020 07:39:09: 11000000 INFO @ Wed, 22 Apr 2020 07:39:16: 16000000 INFO @ Wed, 22 Apr 2020 07:39:17: 8000000 INFO @ Wed, 22 Apr 2020 07:39:17: 12000000 INFO @ Wed, 22 Apr 2020 07:39:24: 17000000 INFO @ Wed, 22 Apr 2020 07:39:25: 13000000 INFO @ Wed, 22 Apr 2020 07:39:25: 9000000 INFO @ Wed, 22 Apr 2020 07:39:32: 14000000 INFO @ Wed, 22 Apr 2020 07:39:33: 18000000 INFO @ Wed, 22 Apr 2020 07:39:33: 10000000 INFO @ Wed, 22 Apr 2020 07:39:39: 15000000 INFO @ Wed, 22 Apr 2020 07:39:41: 19000000 INFO @ Wed, 22 Apr 2020 07:39:42: 11000000 INFO @ Wed, 22 Apr 2020 07:39:47: 16000000 INFO @ Wed, 22 Apr 2020 07:39:49: 20000000 INFO @ Wed, 22 Apr 2020 07:39:50: 12000000 INFO @ Wed, 22 Apr 2020 07:39:55: 17000000 INFO @ Wed, 22 Apr 2020 07:39:57: 21000000 INFO @ Wed, 22 Apr 2020 07:39:58: 13000000 INFO @ Wed, 22 Apr 2020 07:40:03: 18000000 INFO @ Wed, 22 Apr 2020 07:40:05: 22000000 INFO @ Wed, 22 Apr 2020 07:40:06: 14000000 INFO @ Wed, 22 Apr 2020 07:40:11: 19000000 INFO @ Wed, 22 Apr 2020 07:40:13: 23000000 INFO @ Wed, 22 Apr 2020 07:40:13: 15000000 INFO @ Wed, 22 Apr 2020 07:40:19: 20000000 INFO @ Wed, 22 Apr 2020 07:40:21: 16000000 INFO @ Wed, 22 Apr 2020 07:40:21: 24000000 INFO @ Wed, 22 Apr 2020 07:40:27: 21000000 INFO @ Wed, 22 Apr 2020 07:40:28: 17000000 INFO @ Wed, 22 Apr 2020 07:40:29: 25000000 INFO @ Wed, 22 Apr 2020 07:40:34: 22000000 INFO @ Wed, 22 Apr 2020 07:40:36: 18000000 INFO @ Wed, 22 Apr 2020 07:40:37: 26000000 INFO @ Wed, 22 Apr 2020 07:40:42: 23000000 INFO @ Wed, 22 Apr 2020 07:40:44: 19000000 INFO @ Wed, 22 Apr 2020 07:40:45: 27000000 INFO @ Wed, 22 Apr 2020 07:40:48: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 07:40:48: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 07:40:48: #1 total tags in treatment: 27325567 INFO @ Wed, 22 Apr 2020 07:40:48: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:40:48: #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 07:40:48: #1 tags after filtering in treatment: 27325471 INFO @ Wed, 22 Apr 2020 07:40:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:40:48: #1 finished! INFO @ Wed, 22 Apr 2020 07:40:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:40:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:40:50: 24000000 INFO @ Wed, 22 Apr 2020 07:40:51: #2 number of paired peaks: 9196 INFO @ Wed, 22 Apr 2020 07:40:51: start model_add_line... INFO @ Wed, 22 Apr 2020 07:40:51: start X-correlation... INFO @ Wed, 22 Apr 2020 07:40:51: end of X-cor INFO @ Wed, 22 Apr 2020 07:40:51: #2 finished! INFO @ Wed, 22 Apr 2020 07:40:51: #2 predicted fragment length is 103 bps INFO @ Wed, 22 Apr 2020 07:40:51: #2 alternative fragment length(s) may be 103 bps INFO @ Wed, 22 Apr 2020 07:40:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.05_model.r WARNING @ Wed, 22 Apr 2020 07:40:51: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:40:51: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Wed, 22 Apr 2020 07:40:51: #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 07:40:51: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:40:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:40:52: 20000000 INFO @ Wed, 22 Apr 2020 07:40:58: 25000000 INFO @ Wed, 22 Apr 2020 07:40:59: 21000000 INFO @ Wed, 22 Apr 2020 07:41:05: 26000000 INFO @ Wed, 22 Apr 2020 07:41:06: 22000000 INFO @ Wed, 22 Apr 2020 07:41:12: 27000000 INFO @ Wed, 22 Apr 2020 07:41:14: 23000000 INFO @ Wed, 22 Apr 2020 07:41:15: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 07:41:15: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 07:41:15: #1 total tags in treatment: 27325567 INFO @ Wed, 22 Apr 2020 07:41:15: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:41:15: #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 07:41:16: #1 tags after filtering in treatment: 27325471 INFO @ Wed, 22 Apr 2020 07:41:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:41:16: #1 finished! INFO @ Wed, 22 Apr 2020 07:41:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:41:18: #2 number of paired peaks: 9196 INFO @ Wed, 22 Apr 2020 07:41:18: start model_add_line... INFO @ Wed, 22 Apr 2020 07:41:18: start X-correlation... INFO @ Wed, 22 Apr 2020 07:41:18: end of X-cor INFO @ Wed, 22 Apr 2020 07:41:18: #2 finished! INFO @ Wed, 22 Apr 2020 07:41:18: #2 predicted fragment length is 103 bps INFO @ Wed, 22 Apr 2020 07:41:18: #2 alternative fragment length(s) may be 103 bps INFO @ Wed, 22 Apr 2020 07:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.10_model.r WARNING @ Wed, 22 Apr 2020 07:41:18: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:41:18: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Wed, 22 Apr 2020 07:41:18: #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 07:41:18: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:41:21: 24000000 INFO @ Wed, 22 Apr 2020 07:41:28: 25000000 INFO @ Wed, 22 Apr 2020 07:41:35: 26000000 INFO @ Wed, 22 Apr 2020 07:41:41: 27000000 INFO @ Wed, 22 Apr 2020 07:41:44: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 07:41:44: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 07:41:44: #1 total tags in treatment: 27325567 INFO @ Wed, 22 Apr 2020 07:41:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:41:44: #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 07:41:44: #1 tags after filtering in treatment: 27325471 INFO @ Wed, 22 Apr 2020 07:41:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:41:44: #1 finished! INFO @ Wed, 22 Apr 2020 07:41:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:41:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:41:47: #2 number of paired peaks: 9196 INFO @ Wed, 22 Apr 2020 07:41:47: start model_add_line... INFO @ Wed, 22 Apr 2020 07:41:47: start X-correlation... INFO @ Wed, 22 Apr 2020 07:41:47: end of X-cor INFO @ Wed, 22 Apr 2020 07:41:47: #2 finished! INFO @ Wed, 22 Apr 2020 07:41:47: #2 predicted fragment length is 103 bps INFO @ Wed, 22 Apr 2020 07:41:47: #2 alternative fragment length(s) may be 103 bps INFO @ Wed, 22 Apr 2020 07:41:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.20_model.r WARNING @ Wed, 22 Apr 2020 07:41:47: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:41:47: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Wed, 22 Apr 2020 07:41:47: #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 07:41:47: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:41:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:41:51: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:42:20: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:42:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:42:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:42:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.05_summits.bed INFO @ Wed, 22 Apr 2020 07:42:24: Done! pass1 - making usageList (84 chroms): 2 millis pass2 - checking and writing primary data (6724 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:42:48: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:42:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:42:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:42:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.10_summits.bed INFO @ Wed, 22 Apr 2020 07:42:51: Done! pass1 - making usageList (56 chroms): 0 millis pass2 - checking and writing primary data (1801 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:43:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:43:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:43:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299290/SRX5299290.20_summits.bed INFO @ Wed, 22 Apr 2020 07:43:19: Done! pass1 - making usageList (41 chroms): 0 millis pass2 - checking and writing primary data (641 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。