Job ID = 14168517 SRX = ERX3978750 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16701462 spots for ERR3975762/ERR3975762.sra Written 16701462 spots for ERR3975762/ERR3975762.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169781 ("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: 00:50:16 16701462 reads; of these: 16701462 (100.00%) were paired; of these: 6175128 (36.97%) aligned concordantly 0 times 6320735 (37.85%) aligned concordantly exactly 1 time 4205599 (25.18%) aligned concordantly >1 times ---- 6175128 pairs aligned concordantly 0 times; of these: 1420408 (23.00%) aligned discordantly 1 time ---- 4754720 pairs aligned 0 times concordantly or discordantly; of these: 9509440 mates make up the pairs; of these: 6573991 (69.13%) aligned 0 times 334602 (3.52%) aligned exactly 1 time 2600847 (27.35%) aligned >1 times 80.32% overall alignment rate Time searching: 00:50:16 Overall time: 00:50:16 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 20 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] 2895429 / 11864719 = 0.2440 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 19:47:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.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 19:47:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:47:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:47:42: 1000000 INFO @ Fri, 10 Dec 2021 19:47:49: 2000000 INFO @ Fri, 10 Dec 2021 19:47:55: 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 19:48:02: 4000000 INFO @ Fri, 10 Dec 2021 19:48:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.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 19:48:04: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:48:04: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:48:09: 5000000 INFO @ Fri, 10 Dec 2021 19:48:12: 1000000 INFO @ Fri, 10 Dec 2021 19:48:17: 6000000 INFO @ Fri, 10 Dec 2021 19:48:20: 2000000 INFO @ Fri, 10 Dec 2021 19:48:25: 7000000 INFO @ Fri, 10 Dec 2021 19:48:27: 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 19:48:32: 8000000 INFO @ Fri, 10 Dec 2021 19:48:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.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 19:48:34: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:48:34: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:48:35: 4000000 INFO @ Fri, 10 Dec 2021 19:48:41: 9000000 INFO @ Fri, 10 Dec 2021 19:48:42: 1000000 INFO @ Fri, 10 Dec 2021 19:48:43: 5000000 INFO @ Fri, 10 Dec 2021 19:48:48: 2000000 INFO @ Fri, 10 Dec 2021 19:48:49: 10000000 INFO @ Fri, 10 Dec 2021 19:48:50: 6000000 INFO @ Fri, 10 Dec 2021 19:48:56: 3000000 INFO @ Fri, 10 Dec 2021 19:48:57: 11000000 INFO @ Fri, 10 Dec 2021 19:48:59: 7000000 INFO @ Fri, 10 Dec 2021 19:49:03: 4000000 INFO @ Fri, 10 Dec 2021 19:49:05: 12000000 INFO @ Fri, 10 Dec 2021 19:49:07: 8000000 INFO @ Fri, 10 Dec 2021 19:49:09: 5000000 INFO @ Fri, 10 Dec 2021 19:49:12: 13000000 INFO @ Fri, 10 Dec 2021 19:49:14: 9000000 INFO @ Fri, 10 Dec 2021 19:49:16: 6000000 INFO @ Fri, 10 Dec 2021 19:49:19: 14000000 INFO @ Fri, 10 Dec 2021 19:49:22: 10000000 INFO @ Fri, 10 Dec 2021 19:49:23: 7000000 INFO @ Fri, 10 Dec 2021 19:49:26: 15000000 INFO @ Fri, 10 Dec 2021 19:49:29: 11000000 INFO @ Fri, 10 Dec 2021 19:49:30: 8000000 INFO @ Fri, 10 Dec 2021 19:49:34: 16000000 INFO @ Fri, 10 Dec 2021 19:49:37: 9000000 INFO @ Fri, 10 Dec 2021 19:49:38: 12000000 INFO @ Fri, 10 Dec 2021 19:49:41: 17000000 INFO @ Fri, 10 Dec 2021 19:49:44: 10000000 INFO @ Fri, 10 Dec 2021 19:49:45: 13000000 INFO @ Fri, 10 Dec 2021 19:49:49: 18000000 INFO @ Fri, 10 Dec 2021 19:49:51: 11000000 INFO @ Fri, 10 Dec 2021 19:49:52: 14000000 INFO @ Fri, 10 Dec 2021 19:49:58: 19000000 INFO @ Fri, 10 Dec 2021 19:49:58: 12000000 INFO @ Fri, 10 Dec 2021 19:50:00: 15000000 INFO @ Fri, 10 Dec 2021 19:50:06: 20000000 INFO @ Fri, 10 Dec 2021 19:50:07: 13000000 INFO @ Fri, 10 Dec 2021 19:50:07: 16000000 INFO @ Fri, 10 Dec 2021 19:50:13: 14000000 INFO @ Fri, 10 Dec 2021 19:50:14: 21000000 INFO @ Fri, 10 Dec 2021 19:50:14: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:50:14: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:50:14: #1 total tags in treatment: 7729393 INFO @ Fri, 10 Dec 2021 19:50:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:50:14: #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 19:50:14: 17000000 INFO @ Fri, 10 Dec 2021 19:50:14: #1 tags after filtering in treatment: 5705019 INFO @ Fri, 10 Dec 2021 19:50:14: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 10 Dec 2021 19:50:14: #1 finished! INFO @ Fri, 10 Dec 2021 19:50:14: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:50:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:50:15: #2 number of paired peaks: 4726 INFO @ Fri, 10 Dec 2021 19:50:15: start model_add_line... INFO @ Fri, 10 Dec 2021 19:50:15: start X-correlation... INFO @ Fri, 10 Dec 2021 19:50:15: end of X-cor INFO @ Fri, 10 Dec 2021 19:50:15: #2 finished! INFO @ Fri, 10 Dec 2021 19:50:15: #2 predicted fragment length is 194 bps INFO @ Fri, 10 Dec 2021 19:50:15: #2 alternative fragment length(s) may be 194 bps INFO @ Fri, 10 Dec 2021 19:50:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.05_model.r WARNING @ Fri, 10 Dec 2021 19:50:15: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:50:15: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Fri, 10 Dec 2021 19:50:15: #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 19:50:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:50:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:50:19: 15000000 INFO @ Fri, 10 Dec 2021 19:50:21: 18000000 INFO @ Fri, 10 Dec 2021 19:50:25: 16000000 INFO @ Fri, 10 Dec 2021 19:50:28: 19000000 INFO @ Fri, 10 Dec 2021 19:50:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:50:32: 17000000 INFO @ Fri, 10 Dec 2021 19:50:35: 20000000 INFO @ Fri, 10 Dec 2021 19:50:38: 18000000 INFO @ Fri, 10 Dec 2021 19:50:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:50:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:50:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.05_summits.bed INFO @ Fri, 10 Dec 2021 19:50:39: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10369 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:50:41: 21000000 INFO @ Fri, 10 Dec 2021 19:50:42: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:50:42: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:50:42: #1 total tags in treatment: 7729393 INFO @ Fri, 10 Dec 2021 19:50:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:50:42: #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 19:50:42: #1 tags after filtering in treatment: 5705019 INFO @ Fri, 10 Dec 2021 19:50:42: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 10 Dec 2021 19:50:42: #1 finished! INFO @ Fri, 10 Dec 2021 19:50:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:50:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:50:43: #2 number of paired peaks: 4726 INFO @ Fri, 10 Dec 2021 19:50:43: start model_add_line... INFO @ Fri, 10 Dec 2021 19:50:43: start X-correlation... INFO @ Fri, 10 Dec 2021 19:50:43: end of X-cor INFO @ Fri, 10 Dec 2021 19:50:43: #2 finished! INFO @ Fri, 10 Dec 2021 19:50:43: #2 predicted fragment length is 194 bps INFO @ Fri, 10 Dec 2021 19:50:43: #2 alternative fragment length(s) may be 194 bps INFO @ Fri, 10 Dec 2021 19:50:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.10_model.r WARNING @ Fri, 10 Dec 2021 19:50:43: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:50:43: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Fri, 10 Dec 2021 19:50:43: #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 19:50:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:50:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:50:45: 19000000 INFO @ Fri, 10 Dec 2021 19:50:51: 20000000 INFO @ Fri, 10 Dec 2021 19:50:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:50:58: 21000000 INFO @ Fri, 10 Dec 2021 19:50:58: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:50:58: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:50:58: #1 total tags in treatment: 7729393 INFO @ Fri, 10 Dec 2021 19:50:58: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:50:58: #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 19:50:59: #1 tags after filtering in treatment: 5705019 INFO @ Fri, 10 Dec 2021 19:50:59: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 10 Dec 2021 19:50:59: #1 finished! INFO @ Fri, 10 Dec 2021 19:50:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:50:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:50:59: #2 number of paired peaks: 4726 INFO @ Fri, 10 Dec 2021 19:50:59: start model_add_line... INFO @ Fri, 10 Dec 2021 19:50:59: start X-correlation... INFO @ Fri, 10 Dec 2021 19:50:59: end of X-cor INFO @ Fri, 10 Dec 2021 19:50:59: #2 finished! INFO @ Fri, 10 Dec 2021 19:50:59: #2 predicted fragment length is 194 bps INFO @ Fri, 10 Dec 2021 19:50:59: #2 alternative fragment length(s) may be 194 bps INFO @ Fri, 10 Dec 2021 19:50:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.20_model.r WARNING @ Fri, 10 Dec 2021 19:50:59: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:50:59: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Fri, 10 Dec 2021 19:50:59: #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 19:50:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:50:59: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:51:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:51:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:51:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.10_summits.bed INFO @ Fri, 10 Dec 2021 19:51:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6446 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:51:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:51:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:51:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:51:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978750/ERX3978750.20_summits.bed INFO @ Fri, 10 Dec 2021 19:51:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2604 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。