Job ID = 14168326 SRX = ERX3978736 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 32371056 spots for ERR3975745/ERR3975745.sra Written 32371056 spots for ERR3975745/ERR3975745.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169574 ("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: 01:00:30 32371056 reads; of these: 32371056 (100.00%) were paired; of these: 15342237 (47.39%) aligned concordantly 0 times 9869872 (30.49%) aligned concordantly exactly 1 time 7158947 (22.12%) aligned concordantly >1 times ---- 15342237 pairs aligned concordantly 0 times; of these: 3190790 (20.80%) aligned discordantly 1 time ---- 12151447 pairs aligned 0 times concordantly or discordantly; of these: 24302894 mates make up the pairs; of these: 18391106 (75.67%) aligned 0 times 699057 (2.88%) aligned exactly 1 time 5212731 (21.45%) aligned >1 times 71.59% overall alignment rate Time searching: 01:00:30 Overall time: 01:00:30 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 32 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] 5663719 / 20061815 = 0.2823 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 18:42:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.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 18:42:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:42:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:42:54: 1000000 INFO @ Fri, 10 Dec 2021 18:43:01: 2000000 INFO @ Fri, 10 Dec 2021 18:43:08: 3000000 INFO @ Fri, 10 Dec 2021 18:43:15: 4000000 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 18:43:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.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 18:43:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:43:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:43:23: 5000000 INFO @ Fri, 10 Dec 2021 18:43:25: 1000000 INFO @ Fri, 10 Dec 2021 18:43:31: 6000000 INFO @ Fri, 10 Dec 2021 18:43:33: 2000000 INFO @ Fri, 10 Dec 2021 18:43:39: 7000000 INFO @ Fri, 10 Dec 2021 18:43:41: 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 18:43:46: 8000000 INFO @ Fri, 10 Dec 2021 18:43:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.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 18:43:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:43:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:43:50: 4000000 INFO @ Fri, 10 Dec 2021 18:43:55: 9000000 INFO @ Fri, 10 Dec 2021 18:43:58: 1000000 INFO @ Fri, 10 Dec 2021 18:43:59: 5000000 INFO @ Fri, 10 Dec 2021 18:44:04: 10000000 INFO @ Fri, 10 Dec 2021 18:44:08: 2000000 INFO @ Fri, 10 Dec 2021 18:44:08: 6000000 INFO @ Fri, 10 Dec 2021 18:44:13: 11000000 INFO @ Fri, 10 Dec 2021 18:44:17: 7000000 INFO @ Fri, 10 Dec 2021 18:44:18: 3000000 INFO @ Fri, 10 Dec 2021 18:44:22: 12000000 INFO @ Fri, 10 Dec 2021 18:44:26: 8000000 INFO @ Fri, 10 Dec 2021 18:44:28: 4000000 INFO @ Fri, 10 Dec 2021 18:44:31: 13000000 INFO @ Fri, 10 Dec 2021 18:44:35: 9000000 INFO @ Fri, 10 Dec 2021 18:44:38: 5000000 INFO @ Fri, 10 Dec 2021 18:44:40: 14000000 INFO @ Fri, 10 Dec 2021 18:44:44: 10000000 INFO @ Fri, 10 Dec 2021 18:44:47: 6000000 INFO @ Fri, 10 Dec 2021 18:44:49: 15000000 INFO @ Fri, 10 Dec 2021 18:44:53: 11000000 INFO @ Fri, 10 Dec 2021 18:44:57: 7000000 INFO @ Fri, 10 Dec 2021 18:44:58: 16000000 INFO @ Fri, 10 Dec 2021 18:45:02: 12000000 INFO @ Fri, 10 Dec 2021 18:45:07: 17000000 INFO @ Fri, 10 Dec 2021 18:45:07: 8000000 INFO @ Fri, 10 Dec 2021 18:45:11: 13000000 INFO @ Fri, 10 Dec 2021 18:45:16: 18000000 INFO @ Fri, 10 Dec 2021 18:45:17: 9000000 INFO @ Fri, 10 Dec 2021 18:45:19: 14000000 INFO @ Fri, 10 Dec 2021 18:45:25: 19000000 INFO @ Fri, 10 Dec 2021 18:45:27: 10000000 INFO @ Fri, 10 Dec 2021 18:45:28: 15000000 INFO @ Fri, 10 Dec 2021 18:45:34: 20000000 INFO @ Fri, 10 Dec 2021 18:45:37: 11000000 INFO @ Fri, 10 Dec 2021 18:45:37: 16000000 INFO @ Fri, 10 Dec 2021 18:45:43: 21000000 INFO @ Fri, 10 Dec 2021 18:45:46: 17000000 INFO @ Fri, 10 Dec 2021 18:45:47: 12000000 INFO @ Fri, 10 Dec 2021 18:45:51: 22000000 INFO @ Fri, 10 Dec 2021 18:45:55: 18000000 INFO @ Fri, 10 Dec 2021 18:45:57: 13000000 INFO @ Fri, 10 Dec 2021 18:46:00: 23000000 INFO @ Fri, 10 Dec 2021 18:46:04: 19000000 INFO @ Fri, 10 Dec 2021 18:46:07: 14000000 INFO @ Fri, 10 Dec 2021 18:46:08: 24000000 INFO @ Fri, 10 Dec 2021 18:46:12: 20000000 INFO @ Fri, 10 Dec 2021 18:46:16: 25000000 INFO @ Fri, 10 Dec 2021 18:46:17: 15000000 INFO @ Fri, 10 Dec 2021 18:46:21: 21000000 INFO @ Fri, 10 Dec 2021 18:46:24: 26000000 INFO @ Fri, 10 Dec 2021 18:46:27: 16000000 INFO @ Fri, 10 Dec 2021 18:46:30: 22000000 INFO @ Fri, 10 Dec 2021 18:46:32: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:46:37: 17000000 INFO @ Fri, 10 Dec 2021 18:46:38: 23000000 INFO @ Fri, 10 Dec 2021 18:46:41: 28000000 INFO @ Fri, 10 Dec 2021 18:46:46: 24000000 INFO @ Fri, 10 Dec 2021 18:46:47: 18000000 INFO @ Fri, 10 Dec 2021 18:46:49: 29000000 INFO @ Fri, 10 Dec 2021 18:46:54: 25000000 INFO @ Fri, 10 Dec 2021 18:46:57: 19000000 INFO @ Fri, 10 Dec 2021 18:46:58: 30000000 INFO @ Fri, 10 Dec 2021 18:47:03: 26000000 INFO @ Fri, 10 Dec 2021 18:47:06: 20000000 INFO @ Fri, 10 Dec 2021 18:47:07: 31000000 INFO @ Fri, 10 Dec 2021 18:47:11: 27000000 INFO @ Fri, 10 Dec 2021 18:47:15: 32000000 INFO @ Fri, 10 Dec 2021 18:47:16: 21000000 INFO @ Fri, 10 Dec 2021 18:47:19: 28000000 INFO @ Fri, 10 Dec 2021 18:47:24: 33000000 INFO @ Fri, 10 Dec 2021 18:47:26: 22000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:47:28: 29000000 INFO @ Fri, 10 Dec 2021 18:47:33: 34000000 INFO @ Fri, 10 Dec 2021 18:47:35: 23000000 INFO @ Fri, 10 Dec 2021 18:47:37: 30000000 INFO @ Fri, 10 Dec 2021 18:47:42: 35000000 INFO @ Fri, 10 Dec 2021 18:47:42: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:47:42: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:47:42: #1 total tags in treatment: 11647294 INFO @ Fri, 10 Dec 2021 18:47:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:47:42: #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 18:47:42: #1 tags after filtering in treatment: 9103443 INFO @ Fri, 10 Dec 2021 18:47:42: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 10 Dec 2021 18:47:42: #1 finished! INFO @ Fri, 10 Dec 2021 18:47:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:47:43: #2 number of paired peaks: 738 WARNING @ Fri, 10 Dec 2021 18:47:43: Fewer paired peaks (738) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 738 pairs to build model! INFO @ Fri, 10 Dec 2021 18:47:43: start model_add_line... INFO @ Fri, 10 Dec 2021 18:47:43: start X-correlation... INFO @ Fri, 10 Dec 2021 18:47:43: end of X-cor INFO @ Fri, 10 Dec 2021 18:47:43: #2 finished! INFO @ Fri, 10 Dec 2021 18:47:43: #2 predicted fragment length is 176 bps INFO @ Fri, 10 Dec 2021 18:47:43: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 10 Dec 2021 18:47:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.05_model.r WARNING @ Fri, 10 Dec 2021 18:47:43: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:47:43: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Fri, 10 Dec 2021 18:47:43: #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 18:47:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:47:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:47:45: 24000000 INFO @ Fri, 10 Dec 2021 18:47:46: 31000000 INFO @ Fri, 10 Dec 2021 18:47:54: 25000000 INFO @ Fri, 10 Dec 2021 18:47:54: 32000000 INFO @ Fri, 10 Dec 2021 18:48:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:48:03: 26000000 INFO @ Fri, 10 Dec 2021 18:48:03: 33000000 INFO @ Fri, 10 Dec 2021 18:48:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:48:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:48:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.05_summits.bed INFO @ Fri, 10 Dec 2021 18:48:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8037 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:48:11: 34000000 INFO @ Fri, 10 Dec 2021 18:48:12: 27000000 INFO @ Fri, 10 Dec 2021 18:48:20: 35000000 INFO @ Fri, 10 Dec 2021 18:48:20: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:48:20: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:48:20: #1 total tags in treatment: 11647294 INFO @ Fri, 10 Dec 2021 18:48:20: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:48:20: #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 18:48:20: #1 tags after filtering in treatment: 9103443 INFO @ Fri, 10 Dec 2021 18:48:20: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 10 Dec 2021 18:48:20: #1 finished! INFO @ Fri, 10 Dec 2021 18:48:20: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:48:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:48:21: #2 number of paired peaks: 738 WARNING @ Fri, 10 Dec 2021 18:48:21: Fewer paired peaks (738) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 738 pairs to build model! INFO @ Fri, 10 Dec 2021 18:48:21: start model_add_line... INFO @ Fri, 10 Dec 2021 18:48:21: start X-correlation... INFO @ Fri, 10 Dec 2021 18:48:21: end of X-cor INFO @ Fri, 10 Dec 2021 18:48:21: #2 finished! INFO @ Fri, 10 Dec 2021 18:48:21: #2 predicted fragment length is 176 bps INFO @ Fri, 10 Dec 2021 18:48:21: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 10 Dec 2021 18:48:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.10_model.r WARNING @ Fri, 10 Dec 2021 18:48:21: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:48:21: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Fri, 10 Dec 2021 18:48:21: #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 18:48:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:48:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:48:21: 28000000 INFO @ Fri, 10 Dec 2021 18:48:30: 29000000 INFO @ Fri, 10 Dec 2021 18:48:39: 30000000 INFO @ Fri, 10 Dec 2021 18:48:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:48:48: 31000000 INFO @ Fri, 10 Dec 2021 18:48:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:48:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:48:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.10_summits.bed INFO @ Fri, 10 Dec 2021 18:48:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4044 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:48:57: 32000000 INFO @ Fri, 10 Dec 2021 18:49:06: 33000000 INFO @ Fri, 10 Dec 2021 18:49:15: 34000000 INFO @ Fri, 10 Dec 2021 18:49:24: 35000000 INFO @ Fri, 10 Dec 2021 18:49:25: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:49:25: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:49:25: #1 total tags in treatment: 11647294 INFO @ Fri, 10 Dec 2021 18:49:25: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:49:25: #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 18:49:25: #1 tags after filtering in treatment: 9103443 INFO @ Fri, 10 Dec 2021 18:49:25: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 10 Dec 2021 18:49:25: #1 finished! INFO @ Fri, 10 Dec 2021 18:49:25: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:49:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:49:25: #2 number of paired peaks: 738 WARNING @ Fri, 10 Dec 2021 18:49:25: Fewer paired peaks (738) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 738 pairs to build model! INFO @ Fri, 10 Dec 2021 18:49:25: start model_add_line... INFO @ Fri, 10 Dec 2021 18:49:25: start X-correlation... INFO @ Fri, 10 Dec 2021 18:49:26: end of X-cor INFO @ Fri, 10 Dec 2021 18:49:26: #2 finished! INFO @ Fri, 10 Dec 2021 18:49:26: #2 predicted fragment length is 176 bps INFO @ Fri, 10 Dec 2021 18:49:26: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 10 Dec 2021 18:49:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.20_model.r WARNING @ Fri, 10 Dec 2021 18:49:26: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:49:26: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Fri, 10 Dec 2021 18:49:26: #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 18:49:26: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:49:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:49:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:49:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:49:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:49:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978736/ERX3978736.20_summits.bed INFO @ Fri, 10 Dec 2021 18:49:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1258 records, 4 fields): 3 millis CompletedMACS2peakCalling