Job ID = 6459313 SRX = SRX6685748 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:07:49 prefetch.2.10.7: 1) Downloading 'SRR9937041'... 2020-06-21T13:07:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:13:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:13:07 prefetch.2.10.7: 1) 'SRR9937041' was downloaded successfully 2020-06-21T13:13:07 prefetch.2.10.7: 'SRR9937041' has 0 unresolved dependencies Read 31048958 spots for SRR9937041/SRR9937041.sra Written 31048958 spots for SRR9937041/SRR9937041.sra 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: 00:11:10 31048958 reads; of these: 31048958 (100.00%) were unpaired; of these: 3148914 (10.14%) aligned 0 times 20080971 (64.68%) aligned exactly 1 time 7819073 (25.18%) aligned >1 times 89.86% overall alignment rate Time searching: 00:11:10 Overall time: 00:11:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 6877178 / 27900044 = 0.2465 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 @ Sun, 21 Jun 2020 22:35:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.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 @ Sun, 21 Jun 2020 22:35:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:35:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:35:35: 1000000 INFO @ Sun, 21 Jun 2020 22:35:43: 2000000 INFO @ Sun, 21 Jun 2020 22:35:51: 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 @ Sun, 21 Jun 2020 22:35:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.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 @ Sun, 21 Jun 2020 22:35:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:35:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:36:00: 4000000 INFO @ Sun, 21 Jun 2020 22:36:06: 1000000 INFO @ Sun, 21 Jun 2020 22:36:09: 5000000 INFO @ Sun, 21 Jun 2020 22:36:14: 2000000 INFO @ Sun, 21 Jun 2020 22:36:18: 6000000 INFO @ Sun, 21 Jun 2020 22:36:23: 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 @ Sun, 21 Jun 2020 22:36:26: 7000000 INFO @ Sun, 21 Jun 2020 22:36:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.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 @ Sun, 21 Jun 2020 22:36:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:36:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:36:31: 4000000 INFO @ Sun, 21 Jun 2020 22:36:35: 8000000 INFO @ Sun, 21 Jun 2020 22:36:37: 1000000 INFO @ Sun, 21 Jun 2020 22:36:40: 5000000 INFO @ Sun, 21 Jun 2020 22:36:44: 9000000 INFO @ Sun, 21 Jun 2020 22:36:46: 2000000 INFO @ Sun, 21 Jun 2020 22:36:48: 6000000 INFO @ Sun, 21 Jun 2020 22:36:54: 10000000 INFO @ Sun, 21 Jun 2020 22:36:56: 3000000 INFO @ Sun, 21 Jun 2020 22:36:57: 7000000 INFO @ Sun, 21 Jun 2020 22:37:03: 11000000 INFO @ Sun, 21 Jun 2020 22:37:05: 4000000 INFO @ Sun, 21 Jun 2020 22:37:05: 8000000 INFO @ Sun, 21 Jun 2020 22:37:12: 12000000 INFO @ Sun, 21 Jun 2020 22:37:14: 9000000 INFO @ Sun, 21 Jun 2020 22:37:14: 5000000 INFO @ Sun, 21 Jun 2020 22:37:21: 13000000 INFO @ Sun, 21 Jun 2020 22:37:22: 10000000 INFO @ Sun, 21 Jun 2020 22:37:23: 6000000 INFO @ Sun, 21 Jun 2020 22:37:30: 14000000 INFO @ Sun, 21 Jun 2020 22:37:30: 11000000 INFO @ Sun, 21 Jun 2020 22:37:32: 7000000 INFO @ Sun, 21 Jun 2020 22:37:39: 15000000 INFO @ Sun, 21 Jun 2020 22:37:39: 12000000 INFO @ Sun, 21 Jun 2020 22:37:42: 8000000 INFO @ Sun, 21 Jun 2020 22:37:47: 13000000 INFO @ Sun, 21 Jun 2020 22:37:48: 16000000 INFO @ Sun, 21 Jun 2020 22:37:50: 9000000 INFO @ Sun, 21 Jun 2020 22:37:56: 14000000 INFO @ Sun, 21 Jun 2020 22:37:57: 17000000 INFO @ Sun, 21 Jun 2020 22:37:59: 10000000 INFO @ Sun, 21 Jun 2020 22:38:04: 15000000 INFO @ Sun, 21 Jun 2020 22:38:06: 18000000 INFO @ Sun, 21 Jun 2020 22:38:08: 11000000 INFO @ Sun, 21 Jun 2020 22:38:13: 16000000 INFO @ Sun, 21 Jun 2020 22:38:15: 19000000 INFO @ Sun, 21 Jun 2020 22:38:17: 12000000 INFO @ Sun, 21 Jun 2020 22:38:21: 17000000 INFO @ Sun, 21 Jun 2020 22:38:24: 20000000 INFO @ Sun, 21 Jun 2020 22:38:26: 13000000 INFO @ Sun, 21 Jun 2020 22:38:29: 18000000 INFO @ Sun, 21 Jun 2020 22:38:33: 21000000 INFO @ Sun, 21 Jun 2020 22:38:33: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:38:33: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:38:33: #1 total tags in treatment: 21022866 INFO @ Sun, 21 Jun 2020 22:38:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:38:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:38:34: #1 tags after filtering in treatment: 21022786 INFO @ Sun, 21 Jun 2020 22:38:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:38:34: #1 finished! INFO @ Sun, 21 Jun 2020 22:38:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:38:34: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:38:35: 14000000 INFO @ Sun, 21 Jun 2020 22:38:36: #2 number of paired peaks: 1389 INFO @ Sun, 21 Jun 2020 22:38:36: start model_add_line... INFO @ Sun, 21 Jun 2020 22:38:36: start X-correlation... INFO @ Sun, 21 Jun 2020 22:38:36: end of X-cor INFO @ Sun, 21 Jun 2020 22:38:36: #2 finished! INFO @ Sun, 21 Jun 2020 22:38:36: #2 predicted fragment length is 117 bps INFO @ Sun, 21 Jun 2020 22:38:36: #2 alternative fragment length(s) may be 4,117 bps INFO @ Sun, 21 Jun 2020 22:38:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.05_model.r WARNING @ Sun, 21 Jun 2020 22:38:36: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:38:36: #2 You may need to consider one of the other alternative d(s): 4,117 WARNING @ Sun, 21 Jun 2020 22:38:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:38:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:38:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:38:38: 19000000 INFO @ Sun, 21 Jun 2020 22:38:44: 15000000 INFO @ Sun, 21 Jun 2020 22:38:46: 20000000 INFO @ Sun, 21 Jun 2020 22:38:53: 16000000 INFO @ Sun, 21 Jun 2020 22:38:54: 21000000 INFO @ Sun, 21 Jun 2020 22:38:55: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:38:55: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:38:55: #1 total tags in treatment: 21022866 INFO @ Sun, 21 Jun 2020 22:38:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:38:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:38:55: #1 tags after filtering in treatment: 21022786 INFO @ Sun, 21 Jun 2020 22:38:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:38:55: #1 finished! INFO @ Sun, 21 Jun 2020 22:38:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:38:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:38:57: #2 number of paired peaks: 1389 INFO @ Sun, 21 Jun 2020 22:38:57: start model_add_line... INFO @ Sun, 21 Jun 2020 22:38:57: start X-correlation... INFO @ Sun, 21 Jun 2020 22:38:57: end of X-cor INFO @ Sun, 21 Jun 2020 22:38:57: #2 finished! INFO @ Sun, 21 Jun 2020 22:38:57: #2 predicted fragment length is 117 bps INFO @ Sun, 21 Jun 2020 22:38:57: #2 alternative fragment length(s) may be 4,117 bps INFO @ Sun, 21 Jun 2020 22:38:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.10_model.r WARNING @ Sun, 21 Jun 2020 22:38:57: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:38:57: #2 You may need to consider one of the other alternative d(s): 4,117 WARNING @ Sun, 21 Jun 2020 22:38:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:38:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:38:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:39:01: 17000000 INFO @ Sun, 21 Jun 2020 22:39:09: 18000000 INFO @ Sun, 21 Jun 2020 22:39:17: 19000000 INFO @ Sun, 21 Jun 2020 22:39:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:39:25: 20000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:39:33: 21000000 INFO @ Sun, 21 Jun 2020 22:39:33: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:39:33: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:39:33: #1 total tags in treatment: 21022866 INFO @ Sun, 21 Jun 2020 22:39:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:39:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:39:34: #1 tags after filtering in treatment: 21022786 INFO @ Sun, 21 Jun 2020 22:39:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:39:34: #1 finished! INFO @ Sun, 21 Jun 2020 22:39:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:39:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:39:35: #2 number of paired peaks: 1389 INFO @ Sun, 21 Jun 2020 22:39:35: start model_add_line... INFO @ Sun, 21 Jun 2020 22:39:35: start X-correlation... INFO @ Sun, 21 Jun 2020 22:39:35: end of X-cor INFO @ Sun, 21 Jun 2020 22:39:35: #2 finished! INFO @ Sun, 21 Jun 2020 22:39:35: #2 predicted fragment length is 117 bps INFO @ Sun, 21 Jun 2020 22:39:35: #2 alternative fragment length(s) may be 4,117 bps INFO @ Sun, 21 Jun 2020 22:39:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.20_model.r WARNING @ Sun, 21 Jun 2020 22:39:35: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:39:35: #2 You may need to consider one of the other alternative d(s): 4,117 WARNING @ Sun, 21 Jun 2020 22:39:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:39:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:39:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:39:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:39:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:39:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:39:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.05_summits.bed INFO @ Sun, 21 Jun 2020 22:39:47: Done! pass1 - making usageList (715 chroms): 2 millis pass2 - checking and writing primary data (8744 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:40:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:40:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:40:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.10_summits.bed INFO @ Sun, 21 Jun 2020 22:40:09: Done! pass1 - making usageList (628 chroms): 3 millis pass2 - checking and writing primary data (6729 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:40:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:40:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:40:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:40:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6685748/SRX6685748.20_summits.bed INFO @ Sun, 21 Jun 2020 22:40:44: Done! pass1 - making usageList (517 chroms): 2 millis pass2 - checking and writing primary data (4799 records, 4 fields): 19 millis CompletedMACS2peakCalling