Job ID = 14167101 SRX = SRX10412063 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24231179 spots for SRR14035727/SRR14035727.sra Written 24231179 spots for SRR14035727/SRR14035727.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167886 ("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: 01:39:33 24231179 reads; of these: 24231179 (100.00%) were paired; of these: 2590041 (10.69%) aligned concordantly 0 times 15605874 (64.40%) aligned concordantly exactly 1 time 6035264 (24.91%) aligned concordantly >1 times ---- 2590041 pairs aligned concordantly 0 times; of these: 455673 (17.59%) aligned discordantly 1 time ---- 2134368 pairs aligned 0 times concordantly or discordantly; of these: 4268736 mates make up the pairs; of these: 3113071 (72.93%) aligned 0 times 425905 (9.98%) aligned exactly 1 time 729760 (17.10%) aligned >1 times 93.58% overall alignment rate Time searching: 01:39:33 Overall time: 01:39:33 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] 4946009 / 22049338 = 0.2243 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 11:51:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.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 11:51:29: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:51:29: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:51:39: 1000000 INFO @ Fri, 10 Dec 2021 11:51:48: 2000000 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 11:51:58: 3000000 INFO @ Fri, 10 Dec 2021 11:51:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.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 11:51:59: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:51:59: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:52:08: 4000000 INFO @ Fri, 10 Dec 2021 11:52:10: 1000000 INFO @ Fri, 10 Dec 2021 11:52:18: 5000000 INFO @ Fri, 10 Dec 2021 11:52:21: 2000000 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 11:52:29: 6000000 INFO @ Fri, 10 Dec 2021 11:52:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.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 11:52:29: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:52:29: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:52:32: 3000000 INFO @ Fri, 10 Dec 2021 11:52:39: 1000000 INFO @ Fri, 10 Dec 2021 11:52:39: 7000000 INFO @ Fri, 10 Dec 2021 11:52:43: 4000000 INFO @ Fri, 10 Dec 2021 11:52:48: 2000000 INFO @ Fri, 10 Dec 2021 11:52:50: 8000000 INFO @ Fri, 10 Dec 2021 11:52:54: 5000000 INFO @ Fri, 10 Dec 2021 11:52:57: 3000000 INFO @ Fri, 10 Dec 2021 11:53:00: 9000000 INFO @ Fri, 10 Dec 2021 11:53:04: 6000000 INFO @ Fri, 10 Dec 2021 11:53:07: 4000000 INFO @ Fri, 10 Dec 2021 11:53:11: 10000000 INFO @ Fri, 10 Dec 2021 11:53:15: 7000000 INFO @ Fri, 10 Dec 2021 11:53:16: 5000000 INFO @ Fri, 10 Dec 2021 11:53:21: 11000000 INFO @ Fri, 10 Dec 2021 11:53:25: 8000000 INFO @ Fri, 10 Dec 2021 11:53:26: 6000000 INFO @ Fri, 10 Dec 2021 11:53:32: 12000000 INFO @ Fri, 10 Dec 2021 11:53:35: 7000000 INFO @ Fri, 10 Dec 2021 11:53:36: 9000000 INFO @ Fri, 10 Dec 2021 11:53:42: 13000000 INFO @ Fri, 10 Dec 2021 11:53:44: 8000000 INFO @ Fri, 10 Dec 2021 11:53:46: 10000000 INFO @ Fri, 10 Dec 2021 11:53:52: 14000000 INFO @ Fri, 10 Dec 2021 11:53:54: 9000000 INFO @ Fri, 10 Dec 2021 11:53:57: 11000000 INFO @ Fri, 10 Dec 2021 11:54:03: 10000000 INFO @ Fri, 10 Dec 2021 11:54:04: 15000000 INFO @ Fri, 10 Dec 2021 11:54:07: 12000000 INFO @ Fri, 10 Dec 2021 11:54:13: 11000000 INFO @ Fri, 10 Dec 2021 11:54:15: 16000000 INFO @ Fri, 10 Dec 2021 11:54:17: 13000000 INFO @ Fri, 10 Dec 2021 11:54:22: 12000000 INFO @ Fri, 10 Dec 2021 11:54:26: 17000000 INFO @ Fri, 10 Dec 2021 11:54:28: 14000000 INFO @ Fri, 10 Dec 2021 11:54:31: 13000000 INFO @ Fri, 10 Dec 2021 11:54:37: 18000000 INFO @ Fri, 10 Dec 2021 11:54:38: 15000000 INFO @ Fri, 10 Dec 2021 11:54:41: 14000000 INFO @ Fri, 10 Dec 2021 11:54:47: 19000000 INFO @ Fri, 10 Dec 2021 11:54:48: 16000000 INFO @ Fri, 10 Dec 2021 11:54:50: 15000000 INFO @ Fri, 10 Dec 2021 11:54:58: 20000000 INFO @ Fri, 10 Dec 2021 11:54:59: 17000000 INFO @ Fri, 10 Dec 2021 11:55:00: 16000000 INFO @ Fri, 10 Dec 2021 11:55:08: 21000000 INFO @ Fri, 10 Dec 2021 11:55:09: 17000000 INFO @ Fri, 10 Dec 2021 11:55:09: 18000000 INFO @ Fri, 10 Dec 2021 11:55:18: 22000000 INFO @ Fri, 10 Dec 2021 11:55:18: 18000000 INFO @ Fri, 10 Dec 2021 11:55:19: 19000000 INFO @ Fri, 10 Dec 2021 11:55:27: 19000000 INFO @ Fri, 10 Dec 2021 11:55:28: 23000000 INFO @ Fri, 10 Dec 2021 11:55:30: 20000000 INFO @ Fri, 10 Dec 2021 11:55:37: 20000000 INFO @ Fri, 10 Dec 2021 11:55:38: 24000000 INFO @ Fri, 10 Dec 2021 11:55:40: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:55:46: 21000000 INFO @ Fri, 10 Dec 2021 11:55:49: 25000000 INFO @ Fri, 10 Dec 2021 11:55:50: 22000000 INFO @ Fri, 10 Dec 2021 11:55:56: 22000000 INFO @ Fri, 10 Dec 2021 11:55:59: 26000000 INFO @ Fri, 10 Dec 2021 11:56:01: 23000000 INFO @ Fri, 10 Dec 2021 11:56:05: 23000000 INFO @ Fri, 10 Dec 2021 11:56:09: 27000000 INFO @ Fri, 10 Dec 2021 11:56:11: 24000000 INFO @ Fri, 10 Dec 2021 11:56:14: 24000000 INFO @ Fri, 10 Dec 2021 11:56:18: 28000000 INFO @ Fri, 10 Dec 2021 11:56:21: 25000000 INFO @ Fri, 10 Dec 2021 11:56:24: 25000000 INFO @ Fri, 10 Dec 2021 11:56:27: 29000000 INFO @ Fri, 10 Dec 2021 11:56:32: 26000000 INFO @ Fri, 10 Dec 2021 11:56:34: 26000000 INFO @ Fri, 10 Dec 2021 11:56:38: 30000000 INFO @ Fri, 10 Dec 2021 11:56:42: 27000000 INFO @ Fri, 10 Dec 2021 11:56:44: 27000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:56:49: 31000000 INFO @ Fri, 10 Dec 2021 11:56:51: 28000000 INFO @ Fri, 10 Dec 2021 11:56:54: 28000000 INFO @ Fri, 10 Dec 2021 11:56:59: 32000000 INFO @ Fri, 10 Dec 2021 11:57:00: 29000000 INFO @ Fri, 10 Dec 2021 11:57:05: 29000000 INFO @ Fri, 10 Dec 2021 11:57:10: 33000000 INFO @ Fri, 10 Dec 2021 11:57:11: 30000000 INFO @ Fri, 10 Dec 2021 11:57:14: 30000000 INFO @ Fri, 10 Dec 2021 11:57:21: 34000000 INFO @ Fri, 10 Dec 2021 11:57:22: 31000000 INFO @ Fri, 10 Dec 2021 11:57:24: 31000000 INFO @ Fri, 10 Dec 2021 11:57:31: 35000000 INFO @ Fri, 10 Dec 2021 11:57:32: 32000000 INFO @ Fri, 10 Dec 2021 11:57:34: 32000000 INFO @ Fri, 10 Dec 2021 11:57:36: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:57:36: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:57:36: #1 total tags in treatment: 16771156 INFO @ Fri, 10 Dec 2021 11:57:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:57:36: #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 11:57:36: #1 tags after filtering in treatment: 15472217 INFO @ Fri, 10 Dec 2021 11:57:36: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 11:57:36: #1 finished! INFO @ Fri, 10 Dec 2021 11:57:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:57:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:57:37: #2 number of paired peaks: 251 WARNING @ Fri, 10 Dec 2021 11:57:37: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Fri, 10 Dec 2021 11:57:37: start model_add_line... INFO @ Fri, 10 Dec 2021 11:57:37: start X-correlation... INFO @ Fri, 10 Dec 2021 11:57:37: end of X-cor INFO @ Fri, 10 Dec 2021 11:57:37: #2 finished! INFO @ Fri, 10 Dec 2021 11:57:37: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 11:57:37: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 10 Dec 2021 11:57:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.05_model.r WARNING @ Fri, 10 Dec 2021 11:57:37: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:57:37: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Fri, 10 Dec 2021 11:57:37: #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 11:57:37: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:57:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:57:43: 33000000 INFO @ Fri, 10 Dec 2021 11:57:45: 33000000 INFO @ Fri, 10 Dec 2021 11:57:54: 34000000 INFO @ Fri, 10 Dec 2021 11:57:55: 34000000 INFO @ Fri, 10 Dec 2021 11:58:04: 35000000 INFO @ Fri, 10 Dec 2021 11:58:05: 35000000 INFO @ Fri, 10 Dec 2021 11:58:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:58:09: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:58:09: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:58:09: #1 total tags in treatment: 16771156 INFO @ Fri, 10 Dec 2021 11:58:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:58:09: #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 11:58:09: #1 tags after filtering in treatment: 15472217 INFO @ Fri, 10 Dec 2021 11:58:09: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 11:58:09: #1 finished! INFO @ Fri, 10 Dec 2021 11:58:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:58:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:58:09: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:58:09: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:58:09: #1 total tags in treatment: 16771156 INFO @ Fri, 10 Dec 2021 11:58:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:58:09: #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 11:58:10: #1 tags after filtering in treatment: 15472217 INFO @ Fri, 10 Dec 2021 11:58:10: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 11:58:10: #1 finished! INFO @ Fri, 10 Dec 2021 11:58:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:58:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:58:10: #2 number of paired peaks: 251 WARNING @ Fri, 10 Dec 2021 11:58:10: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Fri, 10 Dec 2021 11:58:10: start model_add_line... INFO @ Fri, 10 Dec 2021 11:58:10: start X-correlation... INFO @ Fri, 10 Dec 2021 11:58:10: end of X-cor INFO @ Fri, 10 Dec 2021 11:58:10: #2 finished! INFO @ Fri, 10 Dec 2021 11:58:10: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 11:58:10: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 10 Dec 2021 11:58:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.10_model.r WARNING @ Fri, 10 Dec 2021 11:58:10: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:58:10: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Fri, 10 Dec 2021 11:58:10: #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 11:58:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:58:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:58:11: #2 number of paired peaks: 251 WARNING @ Fri, 10 Dec 2021 11:58:11: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Fri, 10 Dec 2021 11:58:11: start model_add_line... INFO @ Fri, 10 Dec 2021 11:58:11: start X-correlation... INFO @ Fri, 10 Dec 2021 11:58:11: end of X-cor INFO @ Fri, 10 Dec 2021 11:58:11: #2 finished! INFO @ Fri, 10 Dec 2021 11:58:11: #2 predicted fragment length is 213 bps INFO @ Fri, 10 Dec 2021 11:58:11: #2 alternative fragment length(s) may be 213 bps INFO @ Fri, 10 Dec 2021 11:58:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.20_model.r WARNING @ Fri, 10 Dec 2021 11:58:11: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:58:11: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Fri, 10 Dec 2021 11:58:11: #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 11:58:11: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:58:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:58:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:58:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:58:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.05_summits.bed INFO @ Fri, 10 Dec 2021 11:58:23: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9476 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:58:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:58:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:58:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:58:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:58:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.10_summits.bed INFO @ Fri, 10 Dec 2021 11:58:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5678 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:58:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:58:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:58:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412063/SRX10412063.20_summits.bed INFO @ Fri, 10 Dec 2021 11:58:57: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2152 records, 4 fields): 4 millis CompletedMACS2peakCalling