Job ID = 6529553 SRX = SRX3159476 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: 00:15:35 48383439 reads; of these: 48383439 (100.00%) were unpaired; of these: 1387811 (2.87%) aligned 0 times 33332260 (68.89%) aligned exactly 1 time 13663368 (28.24%) aligned >1 times 97.13% overall alignment rate Time searching: 00:15:35 Overall time: 00:15:35 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 20 files... [bam_rmdupse_core] 8978030 / 46995628 = 0.1910 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 02:47:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.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 02:47:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:11: 1000000 INFO @ Tue, 30 Jun 2020 02:47:18: 2000000 INFO @ Tue, 30 Jun 2020 02:47:25: 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 02:47:33: 4000000 INFO @ Tue, 30 Jun 2020 02:47:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.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 02:47:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:40: 5000000 INFO @ Tue, 30 Jun 2020 02:47:42: 1000000 INFO @ Tue, 30 Jun 2020 02:47:48: 6000000 INFO @ Tue, 30 Jun 2020 02:47:50: 2000000 INFO @ Tue, 30 Jun 2020 02:47:55: 7000000 INFO @ Tue, 30 Jun 2020 02:47:58: 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 02:48:03: 8000000 INFO @ Tue, 30 Jun 2020 02:48:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.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 02:48:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:48:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:48:05: 4000000 INFO @ Tue, 30 Jun 2020 02:48:11: 9000000 INFO @ Tue, 30 Jun 2020 02:48:12: 1000000 INFO @ Tue, 30 Jun 2020 02:48:13: 5000000 INFO @ Tue, 30 Jun 2020 02:48:18: 10000000 INFO @ Tue, 30 Jun 2020 02:48:20: 2000000 INFO @ Tue, 30 Jun 2020 02:48:21: 6000000 INFO @ Tue, 30 Jun 2020 02:48:27: 11000000 INFO @ Tue, 30 Jun 2020 02:48:28: 3000000 INFO @ Tue, 30 Jun 2020 02:48:29: 7000000 INFO @ Tue, 30 Jun 2020 02:48:35: 12000000 INFO @ Tue, 30 Jun 2020 02:48:36: 4000000 INFO @ Tue, 30 Jun 2020 02:48:37: 8000000 INFO @ Tue, 30 Jun 2020 02:48:43: 13000000 INFO @ Tue, 30 Jun 2020 02:48:44: 5000000 INFO @ Tue, 30 Jun 2020 02:48:45: 9000000 INFO @ Tue, 30 Jun 2020 02:48:50: 14000000 INFO @ Tue, 30 Jun 2020 02:48:52: 6000000 INFO @ Tue, 30 Jun 2020 02:48:53: 10000000 INFO @ Tue, 30 Jun 2020 02:48:58: 15000000 INFO @ Tue, 30 Jun 2020 02:49:00: 7000000 INFO @ Tue, 30 Jun 2020 02:49:01: 11000000 INFO @ Tue, 30 Jun 2020 02:49:07: 16000000 INFO @ Tue, 30 Jun 2020 02:49:08: 12000000 INFO @ Tue, 30 Jun 2020 02:49:08: 8000000 INFO @ Tue, 30 Jun 2020 02:49:15: 17000000 INFO @ Tue, 30 Jun 2020 02:49:16: 13000000 INFO @ Tue, 30 Jun 2020 02:49:16: 9000000 INFO @ Tue, 30 Jun 2020 02:49:22: 18000000 INFO @ Tue, 30 Jun 2020 02:49:24: 14000000 INFO @ Tue, 30 Jun 2020 02:49:24: 10000000 INFO @ Tue, 30 Jun 2020 02:49:30: 19000000 INFO @ Tue, 30 Jun 2020 02:49:32: 15000000 INFO @ Tue, 30 Jun 2020 02:49:32: 11000000 INFO @ Tue, 30 Jun 2020 02:49:38: 20000000 INFO @ Tue, 30 Jun 2020 02:49:39: 16000000 INFO @ Tue, 30 Jun 2020 02:49:40: 12000000 INFO @ Tue, 30 Jun 2020 02:49:45: 21000000 INFO @ Tue, 30 Jun 2020 02:49:47: 17000000 INFO @ Tue, 30 Jun 2020 02:49:48: 13000000 INFO @ Tue, 30 Jun 2020 02:49:53: 22000000 INFO @ Tue, 30 Jun 2020 02:49:55: 18000000 INFO @ Tue, 30 Jun 2020 02:49:55: 14000000 INFO @ Tue, 30 Jun 2020 02:50:01: 23000000 INFO @ Tue, 30 Jun 2020 02:50:02: 19000000 INFO @ Tue, 30 Jun 2020 02:50:03: 15000000 INFO @ Tue, 30 Jun 2020 02:50:09: 24000000 INFO @ Tue, 30 Jun 2020 02:50:10: 20000000 INFO @ Tue, 30 Jun 2020 02:50:11: 16000000 INFO @ Tue, 30 Jun 2020 02:50:16: 25000000 INFO @ Tue, 30 Jun 2020 02:50:17: 21000000 INFO @ Tue, 30 Jun 2020 02:50:18: 17000000 INFO @ Tue, 30 Jun 2020 02:50:24: 26000000 INFO @ Tue, 30 Jun 2020 02:50:25: 22000000 INFO @ Tue, 30 Jun 2020 02:50:26: 18000000 INFO @ Tue, 30 Jun 2020 02:50:32: 27000000 INFO @ Tue, 30 Jun 2020 02:50:33: 23000000 INFO @ Tue, 30 Jun 2020 02:50:33: 19000000 INFO @ Tue, 30 Jun 2020 02:50:39: 28000000 INFO @ Tue, 30 Jun 2020 02:50:41: 20000000 INFO @ Tue, 30 Jun 2020 02:50:41: 24000000 INFO @ Tue, 30 Jun 2020 02:50:47: 29000000 INFO @ Tue, 30 Jun 2020 02:50:48: 21000000 INFO @ Tue, 30 Jun 2020 02:50:49: 25000000 INFO @ Tue, 30 Jun 2020 02:50:54: 30000000 INFO @ Tue, 30 Jun 2020 02:50:56: 22000000 INFO @ Tue, 30 Jun 2020 02:50:57: 26000000 INFO @ Tue, 30 Jun 2020 02:51:03: 31000000 INFO @ Tue, 30 Jun 2020 02:51:04: 23000000 INFO @ Tue, 30 Jun 2020 02:51:05: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:51:11: 32000000 INFO @ Tue, 30 Jun 2020 02:51:12: 24000000 INFO @ Tue, 30 Jun 2020 02:51:13: 28000000 INFO @ Tue, 30 Jun 2020 02:51:18: 33000000 INFO @ Tue, 30 Jun 2020 02:51:19: 25000000 INFO @ Tue, 30 Jun 2020 02:51:20: 29000000 INFO @ Tue, 30 Jun 2020 02:51:26: 34000000 INFO @ Tue, 30 Jun 2020 02:51:27: 26000000 INFO @ Tue, 30 Jun 2020 02:51:28: 30000000 INFO @ Tue, 30 Jun 2020 02:51:33: 35000000 INFO @ Tue, 30 Jun 2020 02:51:35: 27000000 INFO @ Tue, 30 Jun 2020 02:51:36: 31000000 INFO @ Tue, 30 Jun 2020 02:51:41: 36000000 INFO @ Tue, 30 Jun 2020 02:51:42: 28000000 INFO @ Tue, 30 Jun 2020 02:51:44: 32000000 INFO @ Tue, 30 Jun 2020 02:51:48: 37000000 INFO @ Tue, 30 Jun 2020 02:51:50: 29000000 INFO @ Tue, 30 Jun 2020 02:51:52: 33000000 INFO @ Tue, 30 Jun 2020 02:51:56: 38000000 INFO @ Tue, 30 Jun 2020 02:51:56: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:51:56: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:51:56: #1 total tags in treatment: 38017598 INFO @ Tue, 30 Jun 2020 02:51:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:51:56: #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 02:51:57: 30000000 INFO @ Tue, 30 Jun 2020 02:51:57: #1 tags after filtering in treatment: 38017598 INFO @ Tue, 30 Jun 2020 02:51:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:51:57: #1 finished! INFO @ Tue, 30 Jun 2020 02:51:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:51:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:51:59: 34000000 INFO @ Tue, 30 Jun 2020 02:52:00: #2 number of paired peaks: 112 WARNING @ Tue, 30 Jun 2020 02:52:00: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Tue, 30 Jun 2020 02:52:00: start model_add_line... INFO @ Tue, 30 Jun 2020 02:52:00: start X-correlation... INFO @ Tue, 30 Jun 2020 02:52:00: end of X-cor INFO @ Tue, 30 Jun 2020 02:52:00: #2 finished! INFO @ Tue, 30 Jun 2020 02:52:00: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 02:52:00: #2 alternative fragment length(s) may be 1,42,46,52 bps INFO @ Tue, 30 Jun 2020 02:52:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.05_model.r WARNING @ Tue, 30 Jun 2020 02:52:00: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:52:00: #2 You may need to consider one of the other alternative d(s): 1,42,46,52 WARNING @ Tue, 30 Jun 2020 02:52:00: #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 02:52:00: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:52:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:52:05: 31000000 INFO @ Tue, 30 Jun 2020 02:52:07: 35000000 INFO @ Tue, 30 Jun 2020 02:52:12: 32000000 INFO @ Tue, 30 Jun 2020 02:52:14: 36000000 INFO @ Tue, 30 Jun 2020 02:52:20: 33000000 INFO @ Tue, 30 Jun 2020 02:52:21: 37000000 INFO @ Tue, 30 Jun 2020 02:52:27: 34000000 INFO @ Tue, 30 Jun 2020 02:52:29: 38000000 INFO @ Tue, 30 Jun 2020 02:52:29: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:52:29: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:52:29: #1 total tags in treatment: 38017598 INFO @ Tue, 30 Jun 2020 02:52:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:52:29: #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 02:52:30: #1 tags after filtering in treatment: 38017598 INFO @ Tue, 30 Jun 2020 02:52:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:52:30: #1 finished! INFO @ Tue, 30 Jun 2020 02:52:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:52:30: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:52:33: #2 number of paired peaks: 112 WARNING @ Tue, 30 Jun 2020 02:52:33: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Tue, 30 Jun 2020 02:52:33: start model_add_line... INFO @ Tue, 30 Jun 2020 02:52:33: start X-correlation... INFO @ Tue, 30 Jun 2020 02:52:33: end of X-cor INFO @ Tue, 30 Jun 2020 02:52:33: #2 finished! INFO @ Tue, 30 Jun 2020 02:52:33: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 02:52:33: #2 alternative fragment length(s) may be 1,42,46,52 bps INFO @ Tue, 30 Jun 2020 02:52:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.10_model.r WARNING @ Tue, 30 Jun 2020 02:52:33: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:52:33: #2 You may need to consider one of the other alternative d(s): 1,42,46,52 WARNING @ Tue, 30 Jun 2020 02:52:33: #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 02:52:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:52:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:52:34: 35000000 INFO @ Tue, 30 Jun 2020 02:52:41: 36000000 INFO @ Tue, 30 Jun 2020 02:52:47: 37000000 INFO @ Tue, 30 Jun 2020 02:52:54: 38000000 INFO @ Tue, 30 Jun 2020 02:52:54: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:52:54: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:52:54: #1 total tags in treatment: 38017598 INFO @ Tue, 30 Jun 2020 02:52:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:52:54: #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 02:52:55: #1 tags after filtering in treatment: 38017598 INFO @ Tue, 30 Jun 2020 02:52:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:52:55: #1 finished! INFO @ Tue, 30 Jun 2020 02:52:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:52:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:52:58: #2 number of paired peaks: 112 WARNING @ Tue, 30 Jun 2020 02:52:58: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Tue, 30 Jun 2020 02:52:58: start model_add_line... INFO @ Tue, 30 Jun 2020 02:52:58: start X-correlation... INFO @ Tue, 30 Jun 2020 02:52:58: end of X-cor INFO @ Tue, 30 Jun 2020 02:52:58: #2 finished! INFO @ Tue, 30 Jun 2020 02:52:58: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 02:52:58: #2 alternative fragment length(s) may be 1,42,46,52 bps INFO @ Tue, 30 Jun 2020 02:52:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.20_model.r WARNING @ Tue, 30 Jun 2020 02:52:58: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:52:58: #2 You may need to consider one of the other alternative d(s): 1,42,46,52 WARNING @ Tue, 30 Jun 2020 02:52:58: #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 02:52:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:52:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:53:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:53:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:53:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.05_summits.bed INFO @ Tue, 30 Jun 2020 02:53:34: Done! pass1 - making usageList (769 chroms): 2 millis pass2 - checking and writing primary data (3444 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:53:37: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:54:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:54:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:54:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:54:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.10_summits.bed INFO @ Tue, 30 Jun 2020 02:54:07: Done! pass1 - making usageList (649 chroms): 1 millis pass2 - checking and writing primary data (2521 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:54:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:54:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:54:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159476/SRX3159476.20_summits.bed INFO @ Tue, 30 Jun 2020 02:54:32: Done! pass1 - making usageList (439 chroms): 1 millis pass2 - checking and writing primary data (1050 records, 4 fields): 13 millis CompletedMACS2peakCalling