Job ID = 14167058 SRX = SRX10412047 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 32053294 spots for SRR14035709/SRR14035709.sra Written 32053294 spots for SRR14035709/SRR14035709.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167652 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:10:05 32053294 reads; of these: 32053294 (100.00%) were paired; of these: 15074648 (47.03%) aligned concordantly 0 times 14912746 (46.52%) aligned concordantly exactly 1 time 2065900 (6.45%) aligned concordantly >1 times ---- 15074648 pairs aligned concordantly 0 times; of these: 5116074 (33.94%) aligned discordantly 1 time ---- 9958574 pairs aligned 0 times concordantly or discordantly; of these: 19917148 mates make up the pairs; of these: 17362208 (87.17%) aligned 0 times 1230355 (6.18%) aligned exactly 1 time 1324585 (6.65%) aligned >1 times 72.92% overall alignment rate Time searching: 01:10:05 Overall time: 01:10:05 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 36 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] 4746267 / 22009195 = 0.2156 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:03:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.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 @ Fri, 10 Dec 2021 11:03:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:03:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:03:31: 1000000 INFO @ Fri, 10 Dec 2021 11:03:39: 2000000 INFO @ Fri, 10 Dec 2021 11:03:47: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:03:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.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 @ Fri, 10 Dec 2021 11:03:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:03:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:03:56: 4000000 INFO @ Fri, 10 Dec 2021 11:04:01: 1000000 INFO @ Fri, 10 Dec 2021 11:04:04: 5000000 INFO @ Fri, 10 Dec 2021 11:04:09: 2000000 INFO @ Fri, 10 Dec 2021 11:04:13: 6000000 INFO @ Fri, 10 Dec 2021 11:04:17: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:04:21: 7000000 INFO @ Fri, 10 Dec 2021 11:04:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.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 @ Fri, 10 Dec 2021 11:04:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:04:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:04:25: 4000000 INFO @ Fri, 10 Dec 2021 11:04:30: 8000000 INFO @ Fri, 10 Dec 2021 11:04:31: 1000000 INFO @ Fri, 10 Dec 2021 11:04:33: 5000000 INFO @ Fri, 10 Dec 2021 11:04:38: 9000000 INFO @ Fri, 10 Dec 2021 11:04:39: 2000000 INFO @ Fri, 10 Dec 2021 11:04:41: 6000000 INFO @ Fri, 10 Dec 2021 11:04:47: 3000000 INFO @ Fri, 10 Dec 2021 11:04:47: 10000000 INFO @ Fri, 10 Dec 2021 11:04:50: 7000000 INFO @ Fri, 10 Dec 2021 11:04:55: 4000000 INFO @ Fri, 10 Dec 2021 11:04:56: 11000000 INFO @ Fri, 10 Dec 2021 11:04:58: 8000000 INFO @ Fri, 10 Dec 2021 11:05:03: 5000000 INFO @ Fri, 10 Dec 2021 11:05:05: 12000000 INFO @ Fri, 10 Dec 2021 11:05:06: 9000000 INFO @ Fri, 10 Dec 2021 11:05:11: 6000000 INFO @ Fri, 10 Dec 2021 11:05:14: 13000000 INFO @ Fri, 10 Dec 2021 11:05:14: 10000000 INFO @ Fri, 10 Dec 2021 11:05:19: 7000000 INFO @ Fri, 10 Dec 2021 11:05:22: 11000000 INFO @ Fri, 10 Dec 2021 11:05:23: 14000000 INFO @ Fri, 10 Dec 2021 11:05:27: 8000000 INFO @ Fri, 10 Dec 2021 11:05:30: 12000000 INFO @ Fri, 10 Dec 2021 11:05:32: 15000000 INFO @ Fri, 10 Dec 2021 11:05:35: 9000000 INFO @ Fri, 10 Dec 2021 11:05:38: 13000000 INFO @ Fri, 10 Dec 2021 11:05:41: 16000000 INFO @ Fri, 10 Dec 2021 11:05:44: 10000000 INFO @ Fri, 10 Dec 2021 11:05:46: 14000000 INFO @ Fri, 10 Dec 2021 11:05:50: 17000000 INFO @ Fri, 10 Dec 2021 11:05:52: 11000000 INFO @ Fri, 10 Dec 2021 11:05:54: 15000000 INFO @ Fri, 10 Dec 2021 11:05:59: 18000000 INFO @ Fri, 10 Dec 2021 11:06:00: 12000000 INFO @ Fri, 10 Dec 2021 11:06:02: 16000000 INFO @ Fri, 10 Dec 2021 11:06:08: 19000000 INFO @ Fri, 10 Dec 2021 11:06:08: 13000000 INFO @ Fri, 10 Dec 2021 11:06:10: 17000000 INFO @ Fri, 10 Dec 2021 11:06:16: 20000000 INFO @ Fri, 10 Dec 2021 11:06:16: 14000000 INFO @ Fri, 10 Dec 2021 11:06:19: 18000000 INFO @ Fri, 10 Dec 2021 11:06:24: 15000000 INFO @ Fri, 10 Dec 2021 11:06:24: 21000000 INFO @ Fri, 10 Dec 2021 11:06:27: 19000000 INFO @ Fri, 10 Dec 2021 11:06:32: 16000000 INFO @ Fri, 10 Dec 2021 11:06:33: 22000000 INFO @ Fri, 10 Dec 2021 11:06:35: 20000000 INFO @ Fri, 10 Dec 2021 11:06:40: 17000000 INFO @ Fri, 10 Dec 2021 11:06:41: 23000000 INFO @ Fri, 10 Dec 2021 11:06:43: 21000000 INFO @ Fri, 10 Dec 2021 11:06:48: 18000000 INFO @ Fri, 10 Dec 2021 11:06:49: 24000000 INFO @ Fri, 10 Dec 2021 11:06:52: 22000000 INFO @ Fri, 10 Dec 2021 11:06:55: 19000000 INFO @ Fri, 10 Dec 2021 11:06:58: 25000000 INFO @ Fri, 10 Dec 2021 11:07:00: 23000000 INFO @ Fri, 10 Dec 2021 11:07:02: 20000000 INFO @ Fri, 10 Dec 2021 11:07:06: 26000000 INFO @ Fri, 10 Dec 2021 11:07:08: 24000000 INFO @ Fri, 10 Dec 2021 11:07:10: 21000000 INFO @ Fri, 10 Dec 2021 11:07:14: 27000000 INFO @ Fri, 10 Dec 2021 11:07:16: 25000000 INFO @ Fri, 10 Dec 2021 11:07:17: 22000000 INFO @ Fri, 10 Dec 2021 11:07:23: 28000000 INFO @ Fri, 10 Dec 2021 11:07:25: 23000000 INFO @ Fri, 10 Dec 2021 11:07:25: 26000000 INFO @ Fri, 10 Dec 2021 11:07:31: 29000000 INFO @ Fri, 10 Dec 2021 11:07:32: 24000000 INFO @ Fri, 10 Dec 2021 11:07:33: 27000000 INFO @ Fri, 10 Dec 2021 11:07:39: 25000000 INFO @ Fri, 10 Dec 2021 11:07:40: 30000000 INFO @ Fri, 10 Dec 2021 11:07:41: 28000000 INFO @ Fri, 10 Dec 2021 11:07:47: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:07:48: 31000000 INFO @ Fri, 10 Dec 2021 11:07:49: 29000000 INFO @ Fri, 10 Dec 2021 11:07:54: 27000000 INFO @ Fri, 10 Dec 2021 11:07:57: 32000000 INFO @ Fri, 10 Dec 2021 11:07:58: 30000000 INFO @ Fri, 10 Dec 2021 11:08:02: 28000000 INFO @ Fri, 10 Dec 2021 11:08:05: 33000000 INFO @ Fri, 10 Dec 2021 11:08:06: 31000000 INFO @ Fri, 10 Dec 2021 11:08:09: 29000000 INFO @ Fri, 10 Dec 2021 11:08:14: 34000000 INFO @ Fri, 10 Dec 2021 11:08:15: 32000000 INFO @ Fri, 10 Dec 2021 11:08:17: 30000000 INFO @ Fri, 10 Dec 2021 11:08:22: 35000000 INFO @ Fri, 10 Dec 2021 11:08:23: 33000000 INFO @ Fri, 10 Dec 2021 11:08:24: 31000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:08:30: 36000000 INFO @ Fri, 10 Dec 2021 11:08:31: 34000000 INFO @ Fri, 10 Dec 2021 11:08:32: 32000000 INFO @ Fri, 10 Dec 2021 11:08:39: 35000000 INFO @ Fri, 10 Dec 2021 11:08:39: 37000000 INFO @ Fri, 10 Dec 2021 11:08:39: 33000000 INFO @ Fri, 10 Dec 2021 11:08:42: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:08:42: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:08:42: #1 total tags in treatment: 13077992 INFO @ Fri, 10 Dec 2021 11:08:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:08:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:08:42: #1 tags after filtering in treatment: 7707902 INFO @ Fri, 10 Dec 2021 11:08:42: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 10 Dec 2021 11:08:42: #1 finished! INFO @ Fri, 10 Dec 2021 11:08:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:08:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:08:43: #2 number of paired peaks: 5901 INFO @ Fri, 10 Dec 2021 11:08:43: start model_add_line... INFO @ Fri, 10 Dec 2021 11:08:43: start X-correlation... INFO @ Fri, 10 Dec 2021 11:08:43: end of X-cor INFO @ Fri, 10 Dec 2021 11:08:43: #2 finished! INFO @ Fri, 10 Dec 2021 11:08:43: #2 predicted fragment length is 251 bps INFO @ Fri, 10 Dec 2021 11:08:43: #2 alternative fragment length(s) may be 251 bps INFO @ Fri, 10 Dec 2021 11:08:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.05_model.r WARNING @ Fri, 10 Dec 2021 11:08:43: #2 Since the d (251) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:08:43: #2 You may need to consider one of the other alternative d(s): 251 WARNING @ Fri, 10 Dec 2021 11:08:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:08:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:08:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:08:47: 34000000 INFO @ Fri, 10 Dec 2021 11:08:47: 36000000 INFO @ Fri, 10 Dec 2021 11:08:54: 35000000 INFO @ Fri, 10 Dec 2021 11:08:56: 37000000 INFO @ Fri, 10 Dec 2021 11:08:58: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:08:58: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:08:58: #1 total tags in treatment: 13077992 INFO @ Fri, 10 Dec 2021 11:08:58: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:08:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:08:59: #1 tags after filtering in treatment: 7707902 INFO @ Fri, 10 Dec 2021 11:08:59: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 10 Dec 2021 11:08:59: #1 finished! INFO @ Fri, 10 Dec 2021 11:08:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:08:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:09:00: #2 number of paired peaks: 5901 INFO @ Fri, 10 Dec 2021 11:09:00: start model_add_line... INFO @ Fri, 10 Dec 2021 11:09:00: start X-correlation... INFO @ Fri, 10 Dec 2021 11:09:00: end of X-cor INFO @ Fri, 10 Dec 2021 11:09:00: #2 finished! INFO @ Fri, 10 Dec 2021 11:09:00: #2 predicted fragment length is 251 bps INFO @ Fri, 10 Dec 2021 11:09:00: #2 alternative fragment length(s) may be 251 bps INFO @ Fri, 10 Dec 2021 11:09:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.10_model.r WARNING @ Fri, 10 Dec 2021 11:09:00: #2 Since the d (251) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:09:00: #2 You may need to consider one of the other alternative d(s): 251 WARNING @ Fri, 10 Dec 2021 11:09:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:09:00: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:09:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:09:01: 36000000 INFO @ Fri, 10 Dec 2021 11:09:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:09:09: 37000000 INFO @ Fri, 10 Dec 2021 11:09:11: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:09:11: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:09:11: #1 total tags in treatment: 13077992 INFO @ Fri, 10 Dec 2021 11:09:11: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:09:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:09:11: #1 tags after filtering in treatment: 7707902 INFO @ Fri, 10 Dec 2021 11:09:11: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 10 Dec 2021 11:09:11: #1 finished! INFO @ Fri, 10 Dec 2021 11:09:11: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:09:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:09:12: #2 number of paired peaks: 5901 INFO @ Fri, 10 Dec 2021 11:09:12: start model_add_line... INFO @ Fri, 10 Dec 2021 11:09:12: start X-correlation... INFO @ Fri, 10 Dec 2021 11:09:12: end of X-cor INFO @ Fri, 10 Dec 2021 11:09:12: #2 finished! INFO @ Fri, 10 Dec 2021 11:09:12: #2 predicted fragment length is 251 bps INFO @ Fri, 10 Dec 2021 11:09:12: #2 alternative fragment length(s) may be 251 bps INFO @ Fri, 10 Dec 2021 11:09:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.20_model.r WARNING @ Fri, 10 Dec 2021 11:09:12: #2 Since the d (251) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:09:12: #2 You may need to consider one of the other alternative d(s): 251 WARNING @ Fri, 10 Dec 2021 11:09:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:09:12: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:09:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:09:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:09:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:09:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.05_summits.bed INFO @ Fri, 10 Dec 2021 11:09:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (10174 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:09:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:09:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:09:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:09:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.10_summits.bed INFO @ Fri, 10 Dec 2021 11:09:31: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7466 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:09:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:09:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:09:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:09:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412047/SRX10412047.20_summits.bed INFO @ Fri, 10 Dec 2021 11:09:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4612 records, 4 fields): 6 millis CompletedMACS2peakCalling