Job ID = 5721079 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T19:16:38 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 ) 2020-04-15T19:19:30 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T19:19:30 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 20,600,396 reads read : 41,200,792 reads written : 41,200,792 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: 02:15:36 20600396 reads; of these: 20600396 (100.00%) were paired; of these: 5694935 (27.64%) aligned concordantly 0 times 4190687 (20.34%) aligned concordantly exactly 1 time 10714774 (52.01%) aligned concordantly >1 times ---- 5694935 pairs aligned concordantly 0 times; of these: 982690 (17.26%) aligned discordantly 1 time ---- 4712245 pairs aligned 0 times concordantly or discordantly; of these: 9424490 mates make up the pairs; of these: 4673650 (49.59%) aligned 0 times 1708353 (18.13%) aligned exactly 1 time 3042487 (32.28%) aligned >1 times 88.66% overall alignment rate Time searching: 02:15:37 Overall time: 02:15:37 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 28 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 8583833 / 15256892 = 0.5626 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 07:19:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.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 07:19:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 07:19:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 07:19:50: 1000000 INFO @ Thu, 16 Apr 2020 07:19:57: 2000000 INFO @ Thu, 16 Apr 2020 07:20:04: 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 @ Thu, 16 Apr 2020 07:20:11: 4000000 INFO @ Thu, 16 Apr 2020 07:20:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.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 07:20:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 07:20:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 07:20:18: 5000000 INFO @ Thu, 16 Apr 2020 07:20:20: 1000000 INFO @ Thu, 16 Apr 2020 07:20:25: 6000000 INFO @ Thu, 16 Apr 2020 07:20:28: 2000000 INFO @ Thu, 16 Apr 2020 07:20:33: 7000000 INFO @ Thu, 16 Apr 2020 07:20:36: 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 @ Thu, 16 Apr 2020 07:20:40: 8000000 INFO @ Thu, 16 Apr 2020 07:20:43: 4000000 INFO @ Thu, 16 Apr 2020 07:20:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.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 07:20:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 07:20:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 07:20:48: 9000000 INFO @ Thu, 16 Apr 2020 07:20:51: 5000000 INFO @ Thu, 16 Apr 2020 07:20:53: 1000000 INFO @ Thu, 16 Apr 2020 07:20:56: 10000000 INFO @ Thu, 16 Apr 2020 07:20:59: 6000000 INFO @ Thu, 16 Apr 2020 07:21:02: 2000000 INFO @ Thu, 16 Apr 2020 07:21:03: 11000000 INFO @ Thu, 16 Apr 2020 07:21:07: 7000000 INFO @ Thu, 16 Apr 2020 07:21:11: 12000000 INFO @ Thu, 16 Apr 2020 07:21:11: 3000000 INFO @ Thu, 16 Apr 2020 07:21:14: 8000000 INFO @ Thu, 16 Apr 2020 07:21:19: 13000000 INFO @ Thu, 16 Apr 2020 07:21:20: 4000000 INFO @ Thu, 16 Apr 2020 07:21:22: 9000000 INFO @ Thu, 16 Apr 2020 07:21:26: 14000000 INFO @ Thu, 16 Apr 2020 07:21:30: 5000000 INFO @ Thu, 16 Apr 2020 07:21:30: 10000000 INFO @ Thu, 16 Apr 2020 07:21:34: 15000000 INFO @ Thu, 16 Apr 2020 07:21:38: 11000000 INFO @ Thu, 16 Apr 2020 07:21:39: 6000000 INFO @ Thu, 16 Apr 2020 07:21:41: 16000000 INFO @ Thu, 16 Apr 2020 07:21:45: 12000000 INFO @ Thu, 16 Apr 2020 07:21:48: 7000000 INFO @ Thu, 16 Apr 2020 07:21:49: 17000000 INFO @ Thu, 16 Apr 2020 07:21:53: 13000000 INFO @ Thu, 16 Apr 2020 07:21:56: 18000000 INFO @ Thu, 16 Apr 2020 07:21:57: 8000000 INFO @ Thu, 16 Apr 2020 07:22:01: 14000000 INFO @ Thu, 16 Apr 2020 07:22:04: 19000000 INFO @ Thu, 16 Apr 2020 07:22:06: 9000000 INFO @ Thu, 16 Apr 2020 07:22:07: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 07:22:07: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 07:22:07: #1 total tags in treatment: 6531462 INFO @ Thu, 16 Apr 2020 07:22:07: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 07:22:07: #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 07:22:07: #1 tags after filtering in treatment: 5049765 INFO @ Thu, 16 Apr 2020 07:22:07: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 16 Apr 2020 07:22:07: #1 finished! INFO @ Thu, 16 Apr 2020 07:22:07: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 07:22:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 07:22:07: #2 number of paired peaks: 5709 INFO @ Thu, 16 Apr 2020 07:22:07: start model_add_line... INFO @ Thu, 16 Apr 2020 07:22:07: start X-correlation... INFO @ Thu, 16 Apr 2020 07:22:07: end of X-cor INFO @ Thu, 16 Apr 2020 07:22:07: #2 finished! INFO @ Thu, 16 Apr 2020 07:22:07: #2 predicted fragment length is 200 bps INFO @ Thu, 16 Apr 2020 07:22:07: #2 alternative fragment length(s) may be 200 bps INFO @ Thu, 16 Apr 2020 07:22:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.05_model.r WARNING @ Thu, 16 Apr 2020 07:22:07: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 07:22:07: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Thu, 16 Apr 2020 07:22:07: #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 07:22:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 07:22:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 07:22:08: 15000000 INFO @ Thu, 16 Apr 2020 07:22:15: 10000000 INFO @ Thu, 16 Apr 2020 07:22:15: 16000000 INFO @ Thu, 16 Apr 2020 07:22:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 07:22:23: 17000000 INFO @ Thu, 16 Apr 2020 07:22:23: 11000000 INFO @ Thu, 16 Apr 2020 07:22:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.05_peaks.xls INFO @ Thu, 16 Apr 2020 07:22:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 07:22:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.05_summits.bed INFO @ Thu, 16 Apr 2020 07:22:26: Done! INFO @ Thu, 16 Apr 2020 07:22:30: 18000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (12382 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 07:22:32: 12000000 INFO @ Thu, 16 Apr 2020 07:22:38: 19000000 INFO @ Thu, 16 Apr 2020 07:22:41: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 07:22:41: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 07:22:41: #1 total tags in treatment: 6531462 INFO @ Thu, 16 Apr 2020 07:22:41: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 07:22:41: #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 07:22:41: #1 tags after filtering in treatment: 5049765 INFO @ Thu, 16 Apr 2020 07:22:41: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 16 Apr 2020 07:22:41: #1 finished! INFO @ Thu, 16 Apr 2020 07:22:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 07:22:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 07:22:41: 13000000 INFO @ Thu, 16 Apr 2020 07:22:41: #2 number of paired peaks: 5709 INFO @ Thu, 16 Apr 2020 07:22:41: start model_add_line... INFO @ Thu, 16 Apr 2020 07:22:41: start X-correlation... INFO @ Thu, 16 Apr 2020 07:22:41: end of X-cor INFO @ Thu, 16 Apr 2020 07:22:41: #2 finished! INFO @ Thu, 16 Apr 2020 07:22:41: #2 predicted fragment length is 200 bps INFO @ Thu, 16 Apr 2020 07:22:41: #2 alternative fragment length(s) may be 200 bps INFO @ Thu, 16 Apr 2020 07:22:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.10_model.r WARNING @ Thu, 16 Apr 2020 07:22:41: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 07:22:41: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Thu, 16 Apr 2020 07:22:41: #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 07:22:41: #3 Call peaks... INFO @ Thu, 16 Apr 2020 07:22:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 07:22:49: 14000000 INFO @ Thu, 16 Apr 2020 07:22:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 07:22:58: 15000000 INFO @ Thu, 16 Apr 2020 07:23:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.10_peaks.xls INFO @ Thu, 16 Apr 2020 07:23:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 07:23:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.10_summits.bed INFO @ Thu, 16 Apr 2020 07:23:00: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9156 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 07:23:06: 16000000 INFO @ Thu, 16 Apr 2020 07:23:15: 17000000 INFO @ Thu, 16 Apr 2020 07:23:23: 18000000 INFO @ Thu, 16 Apr 2020 07:23:31: 19000000 INFO @ Thu, 16 Apr 2020 07:23:34: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 07:23:34: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 07:23:34: #1 total tags in treatment: 6531462 INFO @ Thu, 16 Apr 2020 07:23:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 07:23:34: #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 07:23:34: #1 tags after filtering in treatment: 5049765 INFO @ Thu, 16 Apr 2020 07:23:34: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 16 Apr 2020 07:23:34: #1 finished! INFO @ Thu, 16 Apr 2020 07:23:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 07:23:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 07:23:35: #2 number of paired peaks: 5709 INFO @ Thu, 16 Apr 2020 07:23:35: start model_add_line... INFO @ Thu, 16 Apr 2020 07:23:35: start X-correlation... INFO @ Thu, 16 Apr 2020 07:23:35: end of X-cor INFO @ Thu, 16 Apr 2020 07:23:35: #2 finished! INFO @ Thu, 16 Apr 2020 07:23:35: #2 predicted fragment length is 200 bps INFO @ Thu, 16 Apr 2020 07:23:35: #2 alternative fragment length(s) may be 200 bps INFO @ Thu, 16 Apr 2020 07:23:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.20_model.r WARNING @ Thu, 16 Apr 2020 07:23:35: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 07:23:35: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Thu, 16 Apr 2020 07:23:35: #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 07:23:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 07:23:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 07:23:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 07:23:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.20_peaks.xls INFO @ Thu, 16 Apr 2020 07:23:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 07:23:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448074/SRX6448074.20_summits.bed INFO @ Thu, 16 Apr 2020 07:23:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5128 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。