Job ID = 14168109 SRX = ERX3978941 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 47642987 spots for ERR3976011/ERR3976011.sra Written 47642987 spots for ERR3976011/ERR3976011.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169649 ("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: 03:24:27 47642987 reads; of these: 47642987 (100.00%) were paired; of these: 6718194 (14.10%) aligned concordantly 0 times 31669666 (66.47%) aligned concordantly exactly 1 time 9255127 (19.43%) aligned concordantly >1 times ---- 6718194 pairs aligned concordantly 0 times; of these: 1046025 (15.57%) aligned discordantly 1 time ---- 5672169 pairs aligned 0 times concordantly or discordantly; of these: 11344338 mates make up the pairs; of these: 6972856 (61.47%) aligned 0 times 2257503 (19.90%) aligned exactly 1 time 2113979 (18.63%) aligned >1 times 92.68% overall alignment rate Time searching: 03:24:27 Overall time: 03:24:27 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] 28733445 / 41778804 = 0.6878 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 19:36:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.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 19:36:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:36:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:37:05: 1000000 INFO @ Fri, 10 Dec 2021 19:37:14: 2000000 INFO @ Fri, 10 Dec 2021 19:37:22: 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 19:37:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.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 19:37:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:37:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:37:31: 4000000 INFO @ Fri, 10 Dec 2021 19:37:39: 1000000 INFO @ Fri, 10 Dec 2021 19:37:40: 5000000 INFO @ Fri, 10 Dec 2021 19:37:49: 6000000 INFO @ Fri, 10 Dec 2021 19:37:52: 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 19:37:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.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 19:37:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:37:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:37:57: 7000000 INFO @ Fri, 10 Dec 2021 19:38:06: 8000000 INFO @ Fri, 10 Dec 2021 19:38:06: 3000000 INFO @ Fri, 10 Dec 2021 19:38:11: 1000000 INFO @ Fri, 10 Dec 2021 19:38:15: 9000000 INFO @ Fri, 10 Dec 2021 19:38:21: 4000000 INFO @ Fri, 10 Dec 2021 19:38:25: 10000000 INFO @ Fri, 10 Dec 2021 19:38:26: 2000000 INFO @ Fri, 10 Dec 2021 19:38:34: 11000000 INFO @ Fri, 10 Dec 2021 19:38:36: 5000000 INFO @ Fri, 10 Dec 2021 19:38:44: 12000000 INFO @ Fri, 10 Dec 2021 19:38:45: 3000000 INFO @ Fri, 10 Dec 2021 19:38:52: 13000000 INFO @ Fri, 10 Dec 2021 19:38:53: 6000000 INFO @ Fri, 10 Dec 2021 19:39:01: 14000000 INFO @ Fri, 10 Dec 2021 19:39:02: 4000000 INFO @ Fri, 10 Dec 2021 19:39:08: 7000000 INFO @ Fri, 10 Dec 2021 19:39:10: 15000000 INFO @ Fri, 10 Dec 2021 19:39:15: 5000000 INFO @ Fri, 10 Dec 2021 19:39:19: 16000000 INFO @ Fri, 10 Dec 2021 19:39:23: 8000000 INFO @ Fri, 10 Dec 2021 19:39:27: 17000000 INFO @ Fri, 10 Dec 2021 19:39:32: 6000000 INFO @ Fri, 10 Dec 2021 19:39:37: 18000000 INFO @ Fri, 10 Dec 2021 19:39:37: 9000000 INFO @ Fri, 10 Dec 2021 19:39:46: 19000000 INFO @ Fri, 10 Dec 2021 19:39:48: 7000000 INFO @ Fri, 10 Dec 2021 19:39:51: 10000000 INFO @ Fri, 10 Dec 2021 19:39:55: 20000000 INFO @ Fri, 10 Dec 2021 19:40:01: 8000000 INFO @ Fri, 10 Dec 2021 19:40:05: 21000000 INFO @ Fri, 10 Dec 2021 19:40:05: 11000000 INFO @ Fri, 10 Dec 2021 19:40:14: 22000000 INFO @ Fri, 10 Dec 2021 19:40:16: 9000000 INFO @ Fri, 10 Dec 2021 19:40:20: 12000000 INFO @ Fri, 10 Dec 2021 19:40:22: 23000000 INFO @ Fri, 10 Dec 2021 19:40:31: 10000000 INFO @ Fri, 10 Dec 2021 19:40:31: 24000000 INFO @ Fri, 10 Dec 2021 19:40:33: 13000000 INFO @ Fri, 10 Dec 2021 19:40:40: 25000000 INFO @ Fri, 10 Dec 2021 19:40:44: 11000000 INFO @ Fri, 10 Dec 2021 19:40:46: 14000000 INFO @ Fri, 10 Dec 2021 19:40:49: 26000000 INFO @ Fri, 10 Dec 2021 19:40:57: 12000000 INFO @ Fri, 10 Dec 2021 19:40:58: 27000000 INFO @ Fri, 10 Dec 2021 19:41:00: 15000000 INFO @ Fri, 10 Dec 2021 19:41:06: 28000000 INFO @ Fri, 10 Dec 2021 19:41:12: 13000000 INFO @ Fri, 10 Dec 2021 19:41:14: 16000000 INFO @ Fri, 10 Dec 2021 19:41:15: 29000000 INFO @ Fri, 10 Dec 2021 19:41:23: 30000000 INFO @ Fri, 10 Dec 2021 19:41:28: 14000000 INFO @ Fri, 10 Dec 2021 19:41:28: 17000000 INFO @ Fri, 10 Dec 2021 19:41:31: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:41:31: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:41:31: #1 total tags in treatment: 12921322 INFO @ Fri, 10 Dec 2021 19:41:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:41:31: #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 19:41:31: #1 tags after filtering in treatment: 11746621 INFO @ Fri, 10 Dec 2021 19:41:31: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 19:41:31: #1 finished! INFO @ Fri, 10 Dec 2021 19:41:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:41:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:41:32: #2 number of paired peaks: 868 WARNING @ Fri, 10 Dec 2021 19:41:32: Fewer paired peaks (868) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 868 pairs to build model! INFO @ Fri, 10 Dec 2021 19:41:32: start model_add_line... INFO @ Fri, 10 Dec 2021 19:41:32: start X-correlation... INFO @ Fri, 10 Dec 2021 19:41:32: end of X-cor INFO @ Fri, 10 Dec 2021 19:41:32: #2 finished! INFO @ Fri, 10 Dec 2021 19:41:32: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Dec 2021 19:41:32: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Dec 2021 19:41:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.05_model.r WARNING @ Fri, 10 Dec 2021 19:41:32: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:41:32: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Fri, 10 Dec 2021 19:41:32: #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 19:41:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:41:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:41:40: 18000000 INFO @ Fri, 10 Dec 2021 19:41:41: 15000000 INFO @ Fri, 10 Dec 2021 19:41:53: 19000000 INFO @ Fri, 10 Dec 2021 19:41:54: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:42:08: 20000000 INFO @ Fri, 10 Dec 2021 19:42:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:42:13: 17000000 INFO @ Fri, 10 Dec 2021 19:42:30: 21000000 INFO @ Fri, 10 Dec 2021 19:42:31: 18000000 INFO @ Fri, 10 Dec 2021 19:42:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:42:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:42:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.05_summits.bed INFO @ Fri, 10 Dec 2021 19:42:35: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (10642 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:42:46: 19000000 INFO @ Fri, 10 Dec 2021 19:42:49: 22000000 INFO @ Fri, 10 Dec 2021 19:43:00: 20000000 INFO @ Fri, 10 Dec 2021 19:43:05: 23000000 INFO @ Fri, 10 Dec 2021 19:43:18: 21000000 INFO @ Fri, 10 Dec 2021 19:43:20: 24000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:43:34: 25000000 INFO @ Fri, 10 Dec 2021 19:43:36: 22000000 INFO @ Fri, 10 Dec 2021 19:43:48: 26000000 INFO @ Fri, 10 Dec 2021 19:43:52: 23000000 INFO @ Fri, 10 Dec 2021 19:44:02: 27000000 INFO @ Fri, 10 Dec 2021 19:44:07: 24000000 INFO @ Fri, 10 Dec 2021 19:44:15: 28000000 INFO @ Fri, 10 Dec 2021 19:44:26: 25000000 INFO @ Fri, 10 Dec 2021 19:44:29: 29000000 INFO @ Fri, 10 Dec 2021 19:44:43: 30000000 INFO @ Fri, 10 Dec 2021 19:44:45: 26000000 INFO @ Fri, 10 Dec 2021 19:44:55: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:44:55: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:44:55: #1 total tags in treatment: 12921322 INFO @ Fri, 10 Dec 2021 19:44:55: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:44:55: #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 19:44:56: #1 tags after filtering in treatment: 11746621 INFO @ Fri, 10 Dec 2021 19:44:56: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 19:44:56: #1 finished! INFO @ Fri, 10 Dec 2021 19:44:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:44:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:44:57: #2 number of paired peaks: 868 WARNING @ Fri, 10 Dec 2021 19:44:57: Fewer paired peaks (868) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 868 pairs to build model! INFO @ Fri, 10 Dec 2021 19:44:57: start model_add_line... INFO @ Fri, 10 Dec 2021 19:44:57: start X-correlation... INFO @ Fri, 10 Dec 2021 19:44:57: end of X-cor INFO @ Fri, 10 Dec 2021 19:44:57: #2 finished! INFO @ Fri, 10 Dec 2021 19:44:57: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Dec 2021 19:44:57: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Dec 2021 19:44:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.10_model.r WARNING @ Fri, 10 Dec 2021 19:44:57: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:44:57: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Fri, 10 Dec 2021 19:44:57: #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 19:44:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:44:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:45:02: 27000000 INFO @ Fri, 10 Dec 2021 19:45:16: 28000000 INFO @ Fri, 10 Dec 2021 19:45:28: 29000000 INFO @ Fri, 10 Dec 2021 19:45:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:45:45: 30000000 INFO @ Fri, 10 Dec 2021 19:45:57: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:45:57: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:45:57: #1 total tags in treatment: 12921322 INFO @ Fri, 10 Dec 2021 19:45:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:45:57: #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 19:45:58: #1 tags after filtering in treatment: 11746621 INFO @ Fri, 10 Dec 2021 19:45:58: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 19:45:58: #1 finished! INFO @ Fri, 10 Dec 2021 19:45:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:45:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:45:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:45:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:45:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.10_summits.bed INFO @ Fri, 10 Dec 2021 19:45:59: Done! INFO @ Fri, 10 Dec 2021 19:45:59: #2 number of paired peaks: 868 WARNING @ Fri, 10 Dec 2021 19:45:59: Fewer paired peaks (868) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 868 pairs to build model! INFO @ Fri, 10 Dec 2021 19:45:59: start model_add_line... INFO @ Fri, 10 Dec 2021 19:45:59: start X-correlation... INFO @ Fri, 10 Dec 2021 19:45:59: end of X-cor INFO @ Fri, 10 Dec 2021 19:45:59: #2 finished! INFO @ Fri, 10 Dec 2021 19:45:59: #2 predicted fragment length is 157 bps INFO @ Fri, 10 Dec 2021 19:45:59: #2 alternative fragment length(s) may be 157 bps INFO @ Fri, 10 Dec 2021 19:45:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.20_model.r pass1 - making usageList (15 chroms): 3 millis WARNING @ Fri, 10 Dec 2021 19:45:59: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:45:59: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Fri, 10 Dec 2021 19:45:59: #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 19:45:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:45:59: #3 Pre-compute pvalue-qvalue table... pass2 - checking and writing primary data (5593 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:46:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:47:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:47:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:47:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978941/ERX3978941.20_summits.bed INFO @ Fri, 10 Dec 2021 19:47:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2005 records, 4 fields): 8 millis CompletedMACS2peakCalling