Job ID = 6529698 SRX = SRX3981690 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:10:13 36401578 reads; of these: 36401578 (100.00%) were unpaired; of these: 1045558 (2.87%) aligned 0 times 27143931 (74.57%) aligned exactly 1 time 8212089 (22.56%) aligned >1 times 97.13% overall alignment rate Time searching: 00:10:13 Overall time: 00:10:13 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 16 files... [bam_rmdupse_core] 5015303 / 35356020 = 0.1419 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 @ Tue, 30 Jun 2020 03:02:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.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 @ Tue, 30 Jun 2020 03:02:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:02:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:02:10: 1000000 INFO @ Tue, 30 Jun 2020 03:02:18: 2000000 INFO @ Tue, 30 Jun 2020 03:02:26: 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 @ Tue, 30 Jun 2020 03:02:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.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 @ Tue, 30 Jun 2020 03:02:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:02:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:02:35: 4000000 INFO @ Tue, 30 Jun 2020 03:02:40: 1000000 INFO @ Tue, 30 Jun 2020 03:02:44: 5000000 INFO @ Tue, 30 Jun 2020 03:02:48: 2000000 INFO @ Tue, 30 Jun 2020 03:02:53: 6000000 INFO @ Tue, 30 Jun 2020 03:02:56: 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 @ Tue, 30 Jun 2020 03:03:01: 7000000 INFO @ Tue, 30 Jun 2020 03:03:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.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 @ Tue, 30 Jun 2020 03:03:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:03:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:03:04: 4000000 INFO @ Tue, 30 Jun 2020 03:03:11: 8000000 INFO @ Tue, 30 Jun 2020 03:03:11: 1000000 INFO @ Tue, 30 Jun 2020 03:03:12: 5000000 INFO @ Tue, 30 Jun 2020 03:03:20: 9000000 INFO @ Tue, 30 Jun 2020 03:03:21: 6000000 INFO @ Tue, 30 Jun 2020 03:03:21: 2000000 INFO @ Tue, 30 Jun 2020 03:03:28: 10000000 INFO @ Tue, 30 Jun 2020 03:03:29: 7000000 INFO @ Tue, 30 Jun 2020 03:03:30: 3000000 INFO @ Tue, 30 Jun 2020 03:03:37: 8000000 INFO @ Tue, 30 Jun 2020 03:03:38: 11000000 INFO @ Tue, 30 Jun 2020 03:03:40: 4000000 INFO @ Tue, 30 Jun 2020 03:03:45: 9000000 INFO @ Tue, 30 Jun 2020 03:03:47: 12000000 INFO @ Tue, 30 Jun 2020 03:03:50: 5000000 INFO @ Tue, 30 Jun 2020 03:03:53: 10000000 INFO @ Tue, 30 Jun 2020 03:03:55: 13000000 INFO @ Tue, 30 Jun 2020 03:03:59: 6000000 INFO @ Tue, 30 Jun 2020 03:04:01: 11000000 INFO @ Tue, 30 Jun 2020 03:04:04: 14000000 INFO @ Tue, 30 Jun 2020 03:04:08: 7000000 INFO @ Tue, 30 Jun 2020 03:04:09: 12000000 INFO @ Tue, 30 Jun 2020 03:04:13: 15000000 INFO @ Tue, 30 Jun 2020 03:04:17: 13000000 INFO @ Tue, 30 Jun 2020 03:04:18: 8000000 INFO @ Tue, 30 Jun 2020 03:04:22: 16000000 INFO @ Tue, 30 Jun 2020 03:04:25: 14000000 INFO @ Tue, 30 Jun 2020 03:04:26: 9000000 INFO @ Tue, 30 Jun 2020 03:04:31: 17000000 INFO @ Tue, 30 Jun 2020 03:04:33: 15000000 INFO @ Tue, 30 Jun 2020 03:04:36: 10000000 INFO @ Tue, 30 Jun 2020 03:04:40: 18000000 INFO @ Tue, 30 Jun 2020 03:04:41: 16000000 INFO @ Tue, 30 Jun 2020 03:04:45: 11000000 INFO @ Tue, 30 Jun 2020 03:04:49: 19000000 INFO @ Tue, 30 Jun 2020 03:04:49: 17000000 INFO @ Tue, 30 Jun 2020 03:04:53: 12000000 INFO @ Tue, 30 Jun 2020 03:04:57: 18000000 INFO @ Tue, 30 Jun 2020 03:04:57: 20000000 INFO @ Tue, 30 Jun 2020 03:05:02: 13000000 INFO @ Tue, 30 Jun 2020 03:05:05: 19000000 INFO @ Tue, 30 Jun 2020 03:05:06: 21000000 INFO @ Tue, 30 Jun 2020 03:05:11: 14000000 INFO @ Tue, 30 Jun 2020 03:05:13: 20000000 INFO @ Tue, 30 Jun 2020 03:05:15: 22000000 INFO @ Tue, 30 Jun 2020 03:05:20: 15000000 INFO @ Tue, 30 Jun 2020 03:05:21: 21000000 INFO @ Tue, 30 Jun 2020 03:05:24: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:05:29: 16000000 INFO @ Tue, 30 Jun 2020 03:05:29: 22000000 INFO @ Tue, 30 Jun 2020 03:05:33: 24000000 INFO @ Tue, 30 Jun 2020 03:05:38: 23000000 INFO @ Tue, 30 Jun 2020 03:05:39: 17000000 INFO @ Tue, 30 Jun 2020 03:05:42: 25000000 INFO @ Tue, 30 Jun 2020 03:05:46: 24000000 INFO @ Tue, 30 Jun 2020 03:05:48: 18000000 INFO @ Tue, 30 Jun 2020 03:05:51: 26000000 INFO @ Tue, 30 Jun 2020 03:05:55: 25000000 INFO @ Tue, 30 Jun 2020 03:05:57: 19000000 INFO @ Tue, 30 Jun 2020 03:06:01: 27000000 INFO @ Tue, 30 Jun 2020 03:06:04: 26000000 INFO @ Tue, 30 Jun 2020 03:06:07: 20000000 INFO @ Tue, 30 Jun 2020 03:06:10: 28000000 INFO @ Tue, 30 Jun 2020 03:06:12: 27000000 INFO @ Tue, 30 Jun 2020 03:06:16: 21000000 INFO @ Tue, 30 Jun 2020 03:06:19: 29000000 INFO @ Tue, 30 Jun 2020 03:06:21: 28000000 INFO @ Tue, 30 Jun 2020 03:06:26: 22000000 INFO @ Tue, 30 Jun 2020 03:06:29: 30000000 INFO @ Tue, 30 Jun 2020 03:06:29: 29000000 INFO @ Tue, 30 Jun 2020 03:06:32: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:06:32: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:06:32: #1 total tags in treatment: 30340717 INFO @ Tue, 30 Jun 2020 03:06:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:06:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:06:33: #1 tags after filtering in treatment: 30340668 INFO @ Tue, 30 Jun 2020 03:06:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:06:33: #1 finished! INFO @ Tue, 30 Jun 2020 03:06:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:06:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:06:35: #2 number of paired peaks: 203 WARNING @ Tue, 30 Jun 2020 03:06:35: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Tue, 30 Jun 2020 03:06:35: start model_add_line... INFO @ Tue, 30 Jun 2020 03:06:35: start X-correlation... INFO @ Tue, 30 Jun 2020 03:06:35: end of X-cor INFO @ Tue, 30 Jun 2020 03:06:35: #2 finished! INFO @ Tue, 30 Jun 2020 03:06:35: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 03:06:35: #2 alternative fragment length(s) may be 1,49,585 bps INFO @ Tue, 30 Jun 2020 03:06:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.05_model.r WARNING @ Tue, 30 Jun 2020 03:06:35: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:06:35: #2 You may need to consider one of the other alternative d(s): 1,49,585 WARNING @ Tue, 30 Jun 2020 03:06:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:06:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:06:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:06:35: 23000000 INFO @ Tue, 30 Jun 2020 03:06:37: 30000000 INFO @ Tue, 30 Jun 2020 03:06:40: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:06:40: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:06:40: #1 total tags in treatment: 30340717 INFO @ Tue, 30 Jun 2020 03:06:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:06:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:06:41: #1 tags after filtering in treatment: 30340668 INFO @ Tue, 30 Jun 2020 03:06:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:06:41: #1 finished! INFO @ Tue, 30 Jun 2020 03:06:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:06:41: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:06:43: 24000000 INFO @ Tue, 30 Jun 2020 03:06:43: #2 number of paired peaks: 203 WARNING @ Tue, 30 Jun 2020 03:06:43: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Tue, 30 Jun 2020 03:06:43: start model_add_line... INFO @ Tue, 30 Jun 2020 03:06:44: start X-correlation... INFO @ Tue, 30 Jun 2020 03:06:44: end of X-cor INFO @ Tue, 30 Jun 2020 03:06:44: #2 finished! INFO @ Tue, 30 Jun 2020 03:06:44: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 03:06:44: #2 alternative fragment length(s) may be 1,49,585 bps INFO @ Tue, 30 Jun 2020 03:06:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.10_model.r WARNING @ Tue, 30 Jun 2020 03:06:44: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:06:44: #2 You may need to consider one of the other alternative d(s): 1,49,585 WARNING @ Tue, 30 Jun 2020 03:06:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:06:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:06:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:06:51: 25000000 INFO @ Tue, 30 Jun 2020 03:06:59: 26000000 INFO @ Tue, 30 Jun 2020 03:07:07: 27000000 INFO @ Tue, 30 Jun 2020 03:07:15: 28000000 INFO @ Tue, 30 Jun 2020 03:07:22: 29000000 INFO @ Tue, 30 Jun 2020 03:07:30: 30000000 INFO @ Tue, 30 Jun 2020 03:07:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:07:32: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:07:32: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:07:32: #1 total tags in treatment: 30340717 INFO @ Tue, 30 Jun 2020 03:07:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:07:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:07:33: #1 tags after filtering in treatment: 30340668 INFO @ Tue, 30 Jun 2020 03:07:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:07:33: #1 finished! INFO @ Tue, 30 Jun 2020 03:07:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:07:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:07:35: #2 number of paired peaks: 203 WARNING @ Tue, 30 Jun 2020 03:07:35: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Tue, 30 Jun 2020 03:07:35: start model_add_line... INFO @ Tue, 30 Jun 2020 03:07:35: start X-correlation... INFO @ Tue, 30 Jun 2020 03:07:35: end of X-cor INFO @ Tue, 30 Jun 2020 03:07:35: #2 finished! INFO @ Tue, 30 Jun 2020 03:07:35: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 03:07:35: #2 alternative fragment length(s) may be 1,49,585 bps INFO @ Tue, 30 Jun 2020 03:07:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.20_model.r WARNING @ Tue, 30 Jun 2020 03:07:35: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:07:35: #2 You may need to consider one of the other alternative d(s): 1,49,585 WARNING @ Tue, 30 Jun 2020 03:07:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:07:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:07:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:07:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:07:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:07:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:07:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.05_summits.bed INFO @ Tue, 30 Jun 2020 03:07:59: Done! pass1 - making usageList (645 chroms): 2 millis pass2 - checking and writing primary data (3358 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:08:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:08:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:08:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.10_summits.bed INFO @ Tue, 30 Jun 2020 03:08:09: Done! pass1 - making usageList (416 chroms): 1 millis pass2 - checking and writing primary data (1384 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:08:30: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:08:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:08:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:08:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981690/SRX3981690.20_summits.bed INFO @ Tue, 30 Jun 2020 03:08:59: Done! pass1 - making usageList (167 chroms): 1 millis pass2 - checking and writing primary data (412 records, 4 fields): 7 millis CompletedMACS2peakCalling