Job ID = 5721089 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T19:41:23 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 ) 2020-04-15T19:41:24 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 : 50,844,759 reads read : 101,689,518 reads written : 50,844,759 reads 0-length : 50,844,759 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: 00:00:00 Multiseed full-index search: 00:19:23 50844759 reads; of these: 50844759 (100.00%) were unpaired; of these: 4579076 (9.01%) aligned 0 times 35519589 (69.86%) aligned exactly 1 time 10746094 (21.14%) aligned >1 times 90.99% overall alignment rate Time searching: 00:19:23 Overall time: 00:19:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 21295824 / 46265683 = 0.4603 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 @ Thu, 16 Apr 2020 05:17:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 05:17:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:17:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:17:40: 1000000 INFO @ Thu, 16 Apr 2020 05:17:45: 2000000 INFO @ Thu, 16 Apr 2020 05:17:51: 3000000 INFO @ Thu, 16 Apr 2020 05:17:56: 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 @ Thu, 16 Apr 2020 05:18:01: 5000000 INFO @ Thu, 16 Apr 2020 05:18:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 05:18:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:18:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:18:07: 6000000 INFO @ Thu, 16 Apr 2020 05:18:10: 1000000 INFO @ Thu, 16 Apr 2020 05:18:12: 7000000 INFO @ Thu, 16 Apr 2020 05:18:16: 2000000 INFO @ Thu, 16 Apr 2020 05:18:18: 8000000 INFO @ Thu, 16 Apr 2020 05:18:22: 3000000 INFO @ Thu, 16 Apr 2020 05:18:23: 9000000 INFO @ Thu, 16 Apr 2020 05:18:27: 4000000 INFO @ Thu, 16 Apr 2020 05:18:29: 10000000 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 @ Thu, 16 Apr 2020 05:18:33: 5000000 INFO @ Thu, 16 Apr 2020 05:18:35: 11000000 INFO @ Thu, 16 Apr 2020 05:18:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 05:18:36: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:18:36: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:18:38: 6000000 INFO @ Thu, 16 Apr 2020 05:18:40: 12000000 INFO @ Thu, 16 Apr 2020 05:18:42: 1000000 INFO @ Thu, 16 Apr 2020 05:18:44: 7000000 INFO @ Thu, 16 Apr 2020 05:18:46: 13000000 INFO @ Thu, 16 Apr 2020 05:18:49: 2000000 INFO @ Thu, 16 Apr 2020 05:18:50: 8000000 INFO @ Thu, 16 Apr 2020 05:18:52: 14000000 INFO @ Thu, 16 Apr 2020 05:18:55: 3000000 INFO @ Thu, 16 Apr 2020 05:18:56: 9000000 INFO @ Thu, 16 Apr 2020 05:18:58: 15000000 INFO @ Thu, 16 Apr 2020 05:19:01: 4000000 INFO @ Thu, 16 Apr 2020 05:19:02: 10000000 INFO @ Thu, 16 Apr 2020 05:19:03: 16000000 INFO @ Thu, 16 Apr 2020 05:19:07: 11000000 INFO @ Thu, 16 Apr 2020 05:19:08: 5000000 INFO @ Thu, 16 Apr 2020 05:19:09: 17000000 INFO @ Thu, 16 Apr 2020 05:19:13: 12000000 INFO @ Thu, 16 Apr 2020 05:19:14: 6000000 INFO @ Thu, 16 Apr 2020 05:19:15: 18000000 INFO @ Thu, 16 Apr 2020 05:19:19: 13000000 INFO @ Thu, 16 Apr 2020 05:19:21: 7000000 INFO @ Thu, 16 Apr 2020 05:19:21: 19000000 INFO @ Thu, 16 Apr 2020 05:19:25: 14000000 INFO @ Thu, 16 Apr 2020 05:19:26: 20000000 INFO @ Thu, 16 Apr 2020 05:19:27: 8000000 INFO @ Thu, 16 Apr 2020 05:19:31: 15000000 INFO @ Thu, 16 Apr 2020 05:19:32: 21000000 INFO @ Thu, 16 Apr 2020 05:19:33: 9000000 INFO @ Thu, 16 Apr 2020 05:19:36: 16000000 INFO @ Thu, 16 Apr 2020 05:19:38: 22000000 INFO @ Thu, 16 Apr 2020 05:19:40: 10000000 INFO @ Thu, 16 Apr 2020 05:19:42: 17000000 INFO @ Thu, 16 Apr 2020 05:19:44: 23000000 INFO @ Thu, 16 Apr 2020 05:19:46: 11000000 INFO @ Thu, 16 Apr 2020 05:19:48: 18000000 INFO @ Thu, 16 Apr 2020 05:19:50: 24000000 INFO @ Thu, 16 Apr 2020 05:19:53: 12000000 INFO @ Thu, 16 Apr 2020 05:19:54: 19000000 INFO @ Thu, 16 Apr 2020 05:19:55: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:19:55: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:19:55: #1 total tags in treatment: 24969859 INFO @ Thu, 16 Apr 2020 05:19:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:19:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:19:56: #1 tags after filtering in treatment: 24969859 INFO @ Thu, 16 Apr 2020 05:19:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:19:56: #1 finished! INFO @ Thu, 16 Apr 2020 05:19:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:19:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:19:57: #2 number of paired peaks: 1518 INFO @ Thu, 16 Apr 2020 05:19:57: start model_add_line... INFO @ Thu, 16 Apr 2020 05:19:58: start X-correlation... INFO @ Thu, 16 Apr 2020 05:19:58: end of X-cor INFO @ Thu, 16 Apr 2020 05:19:58: #2 finished! INFO @ Thu, 16 Apr 2020 05:19:58: #2 predicted fragment length is 122 bps INFO @ Thu, 16 Apr 2020 05:19:58: #2 alternative fragment length(s) may be 122 bps INFO @ Thu, 16 Apr 2020 05:19:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.05_model.r WARNING @ Thu, 16 Apr 2020 05:19:58: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:19:58: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Thu, 16 Apr 2020 05:19:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:19:58: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:19:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:19:59: 13000000 INFO @ Thu, 16 Apr 2020 05:20:00: 20000000 INFO @ Thu, 16 Apr 2020 05:20:05: 14000000 INFO @ Thu, 16 Apr 2020 05:20:05: 21000000 INFO @ Thu, 16 Apr 2020 05:20:11: 22000000 INFO @ Thu, 16 Apr 2020 05:20:12: 15000000 INFO @ Thu, 16 Apr 2020 05:20:17: 23000000 INFO @ Thu, 16 Apr 2020 05:20:18: 16000000 INFO @ Thu, 16 Apr 2020 05:20:23: 24000000 INFO @ Thu, 16 Apr 2020 05:20:24: 17000000 INFO @ Thu, 16 Apr 2020 05:20:28: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:20:28: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:20:28: #1 total tags in treatment: 24969859 INFO @ Thu, 16 Apr 2020 05:20:28: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:20:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:20:29: #1 tags after filtering in treatment: 24969859 INFO @ Thu, 16 Apr 2020 05:20:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:20:29: #1 finished! INFO @ Thu, 16 Apr 2020 05:20:29: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:20:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:20:31: #2 number of paired peaks: 1518 INFO @ Thu, 16 Apr 2020 05:20:31: start model_add_line... INFO @ Thu, 16 Apr 2020 05:20:31: start X-correlation... INFO @ Thu, 16 Apr 2020 05:20:31: end of X-cor INFO @ Thu, 16 Apr 2020 05:20:31: #2 finished! INFO @ Thu, 16 Apr 2020 05:20:31: #2 predicted fragment length is 122 bps INFO @ Thu, 16 Apr 2020 05:20:31: #2 alternative fragment length(s) may be 122 bps INFO @ Thu, 16 Apr 2020 05:20:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.10_model.r WARNING @ Thu, 16 Apr 2020 05:20:31: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:20:31: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Thu, 16 Apr 2020 05:20:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:20:31: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:20:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:20:31: 18000000 INFO @ Thu, 16 Apr 2020 05:20:37: 19000000 INFO @ Thu, 16 Apr 2020 05:20:44: 20000000 INFO @ Thu, 16 Apr 2020 05:20:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:20:50: 21000000 INFO @ Thu, 16 Apr 2020 05:20:56: 22000000 INFO @ Thu, 16 Apr 2020 05:21:02: 23000000 INFO @ Thu, 16 Apr 2020 05:21:09: 24000000 INFO @ Thu, 16 Apr 2020 05:21:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:21:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:21:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.05_summits.bed INFO @ Thu, 16 Apr 2020 05:21:11: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (20100 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:21:15: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:21:15: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:21:15: #1 total tags in treatment: 24969859 INFO @ Thu, 16 Apr 2020 05:21:15: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:21:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:21:15: #1 tags after filtering in treatment: 24969859 INFO @ Thu, 16 Apr 2020 05:21:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:21:15: #1 finished! INFO @ Thu, 16 Apr 2020 05:21:15: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:21:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:21:17: #2 number of paired peaks: 1518 INFO @ Thu, 16 Apr 2020 05:21:17: start model_add_line... INFO @ Thu, 16 Apr 2020 05:21:17: start X-correlation... INFO @ Thu, 16 Apr 2020 05:21:17: end of X-cor INFO @ Thu, 16 Apr 2020 05:21:17: #2 finished! INFO @ Thu, 16 Apr 2020 05:21:17: #2 predicted fragment length is 122 bps INFO @ Thu, 16 Apr 2020 05:21:17: #2 alternative fragment length(s) may be 122 bps INFO @ Thu, 16 Apr 2020 05:21:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.20_model.r WARNING @ Thu, 16 Apr 2020 05:21:17: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:21:17: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Thu, 16 Apr 2020 05:21:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 05:21:17: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:21:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:21:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:21:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:21:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:21:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.10_summits.bed INFO @ Thu, 16 Apr 2020 05:21:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (15486 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:22:06: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:22:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:22:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:22:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685744/SRX6685744.20_summits.bed INFO @ Thu, 16 Apr 2020 05:22:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (10794 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。