Job ID = 14168260 SRX = ERX3978729 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25130542 spots for ERR3975738/ERR3975738.sra Written 25130542 spots for ERR3975738/ERR3975738.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169438 ("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: 00:51:52 25130542 reads; of these: 25130542 (100.00%) were paired; of these: 9495928 (37.79%) aligned concordantly 0 times 8586525 (34.17%) aligned concordantly exactly 1 time 7048089 (28.05%) aligned concordantly >1 times ---- 9495928 pairs aligned concordantly 0 times; of these: 2420934 (25.49%) aligned discordantly 1 time ---- 7074994 pairs aligned 0 times concordantly or discordantly; of these: 14149988 mates make up the pairs; of these: 9279541 (65.58%) aligned 0 times 483608 (3.42%) aligned exactly 1 time 4386839 (31.00%) aligned >1 times 81.54% overall alignment rate Time searching: 00:51:52 Overall time: 00:51:52 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 28 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] 5589776 / 17932352 = 0.3117 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 17:47:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.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 17:47:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:47:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:48:04: 1000000 INFO @ Fri, 10 Dec 2021 17:48:12: 2000000 INFO @ Fri, 10 Dec 2021 17:48:19: 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 17:48:26: 4000000 INFO @ Fri, 10 Dec 2021 17:48:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.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 17:48:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:48:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:48:35: 5000000 INFO @ Fri, 10 Dec 2021 17:48:36: 1000000 INFO @ Fri, 10 Dec 2021 17:48:44: 6000000 INFO @ Fri, 10 Dec 2021 17:48:45: 2000000 INFO @ Fri, 10 Dec 2021 17:48:53: 7000000 INFO @ Fri, 10 Dec 2021 17:48:54: 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 17:48:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.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 17:48:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 17:48:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 17:49:02: 8000000 INFO @ Fri, 10 Dec 2021 17:49:03: 4000000 INFO @ Fri, 10 Dec 2021 17:49:06: 1000000 INFO @ Fri, 10 Dec 2021 17:49:11: 9000000 INFO @ Fri, 10 Dec 2021 17:49:12: 5000000 INFO @ Fri, 10 Dec 2021 17:49:15: 2000000 INFO @ Fri, 10 Dec 2021 17:49:20: 10000000 INFO @ Fri, 10 Dec 2021 17:49:21: 6000000 INFO @ Fri, 10 Dec 2021 17:49:24: 3000000 INFO @ Fri, 10 Dec 2021 17:49:29: 11000000 INFO @ Fri, 10 Dec 2021 17:49:31: 7000000 INFO @ Fri, 10 Dec 2021 17:49:33: 4000000 INFO @ Fri, 10 Dec 2021 17:49:38: 12000000 INFO @ Fri, 10 Dec 2021 17:49:40: 8000000 INFO @ Fri, 10 Dec 2021 17:49:43: 5000000 INFO @ Fri, 10 Dec 2021 17:49:47: 13000000 INFO @ Fri, 10 Dec 2021 17:49:49: 9000000 INFO @ Fri, 10 Dec 2021 17:49:52: 6000000 INFO @ Fri, 10 Dec 2021 17:49:56: 14000000 INFO @ Fri, 10 Dec 2021 17:49:58: 10000000 INFO @ Fri, 10 Dec 2021 17:50:01: 7000000 INFO @ Fri, 10 Dec 2021 17:50:05: 15000000 INFO @ Fri, 10 Dec 2021 17:50:07: 11000000 INFO @ Fri, 10 Dec 2021 17:50:10: 8000000 INFO @ Fri, 10 Dec 2021 17:50:14: 16000000 INFO @ Fri, 10 Dec 2021 17:50:16: 12000000 INFO @ Fri, 10 Dec 2021 17:50:19: 9000000 INFO @ Fri, 10 Dec 2021 17:50:23: 17000000 INFO @ Fri, 10 Dec 2021 17:50:25: 13000000 INFO @ Fri, 10 Dec 2021 17:50:28: 10000000 INFO @ Fri, 10 Dec 2021 17:50:32: 18000000 INFO @ Fri, 10 Dec 2021 17:50:34: 14000000 INFO @ Fri, 10 Dec 2021 17:50:38: 11000000 INFO @ Fri, 10 Dec 2021 17:50:41: 19000000 INFO @ Fri, 10 Dec 2021 17:50:43: 15000000 INFO @ Fri, 10 Dec 2021 17:50:47: 12000000 INFO @ Fri, 10 Dec 2021 17:50:50: 20000000 INFO @ Fri, 10 Dec 2021 17:50:52: 16000000 INFO @ Fri, 10 Dec 2021 17:50:56: 13000000 INFO @ Fri, 10 Dec 2021 17:50:58: 21000000 INFO @ Fri, 10 Dec 2021 17:51:02: 17000000 INFO @ Fri, 10 Dec 2021 17:51:05: 14000000 INFO @ Fri, 10 Dec 2021 17:51:07: 22000000 INFO @ Fri, 10 Dec 2021 17:51:11: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 17:51:14: 15000000 INFO @ Fri, 10 Dec 2021 17:51:16: 23000000 INFO @ Fri, 10 Dec 2021 17:51:20: 19000000 INFO @ Fri, 10 Dec 2021 17:51:24: 16000000 INFO @ Fri, 10 Dec 2021 17:51:25: 24000000 INFO @ Fri, 10 Dec 2021 17:51:29: 20000000 INFO @ Fri, 10 Dec 2021 17:51:34: 17000000 INFO @ Fri, 10 Dec 2021 17:51:35: 25000000 INFO @ Fri, 10 Dec 2021 17:51:38: 21000000 INFO @ Fri, 10 Dec 2021 17:51:43: 18000000 INFO @ Fri, 10 Dec 2021 17:51:44: 26000000 INFO @ Fri, 10 Dec 2021 17:51:47: 22000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 17:51:52: 19000000 INFO @ Fri, 10 Dec 2021 17:51:53: 27000000 INFO @ Fri, 10 Dec 2021 17:51:56: 23000000 INFO @ Fri, 10 Dec 2021 17:52:01: 20000000 INFO @ Fri, 10 Dec 2021 17:52:03: 28000000 INFO @ Fri, 10 Dec 2021 17:52:05: 24000000 INFO @ Fri, 10 Dec 2021 17:52:10: 21000000 INFO @ Fri, 10 Dec 2021 17:52:12: 29000000 INFO @ Fri, 10 Dec 2021 17:52:15: 25000000 INFO @ Fri, 10 Dec 2021 17:52:19: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 17:52:19: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 17:52:19: #1 total tags in treatment: 10241091 INFO @ Fri, 10 Dec 2021 17:52:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:52:19: #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 17:52:19: 22000000 INFO @ Fri, 10 Dec 2021 17:52:20: #1 tags after filtering in treatment: 7331728 INFO @ Fri, 10 Dec 2021 17:52:20: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 17:52:20: #1 finished! INFO @ Fri, 10 Dec 2021 17:52:20: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:52:20: #2 number of paired peaks: 3960 INFO @ Fri, 10 Dec 2021 17:52:20: start model_add_line... INFO @ Fri, 10 Dec 2021 17:52:20: start X-correlation... INFO @ Fri, 10 Dec 2021 17:52:20: end of X-cor INFO @ Fri, 10 Dec 2021 17:52:20: #2 finished! INFO @ Fri, 10 Dec 2021 17:52:20: #2 predicted fragment length is 201 bps INFO @ Fri, 10 Dec 2021 17:52:20: #2 alternative fragment length(s) may be 201 bps INFO @ Fri, 10 Dec 2021 17:52:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.05_model.r WARNING @ Fri, 10 Dec 2021 17:52:20: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:52:20: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Fri, 10 Dec 2021 17:52:20: #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 17:52:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:52:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:52:24: 26000000 INFO @ Fri, 10 Dec 2021 17:52:28: 23000000 INFO @ Fri, 10 Dec 2021 17:52:33: 27000000 INFO @ Fri, 10 Dec 2021 17:52:37: 24000000 INFO @ Fri, 10 Dec 2021 17:52:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:52:42: 28000000 INFO @ Fri, 10 Dec 2021 17:52:46: 25000000 INFO @ Fri, 10 Dec 2021 17:52:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.05_peaks.xls INFO @ Fri, 10 Dec 2021 17:52:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:52:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.05_summits.bed INFO @ Fri, 10 Dec 2021 17:52:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11169 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:52:51: 29000000 INFO @ Fri, 10 Dec 2021 17:52:55: 26000000 INFO @ Fri, 10 Dec 2021 17:52:58: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 17:52:58: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 17:52:58: #1 total tags in treatment: 10241091 INFO @ Fri, 10 Dec 2021 17:52:58: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:52:58: #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 17:52:58: #1 tags after filtering in treatment: 7331728 INFO @ Fri, 10 Dec 2021 17:52:58: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 17:52:58: #1 finished! INFO @ Fri, 10 Dec 2021 17:52:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:52:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:52:59: #2 number of paired peaks: 3960 INFO @ Fri, 10 Dec 2021 17:52:59: start model_add_line... INFO @ Fri, 10 Dec 2021 17:52:59: start X-correlation... INFO @ Fri, 10 Dec 2021 17:52:59: end of X-cor INFO @ Fri, 10 Dec 2021 17:52:59: #2 finished! INFO @ Fri, 10 Dec 2021 17:52:59: #2 predicted fragment length is 201 bps INFO @ Fri, 10 Dec 2021 17:52:59: #2 alternative fragment length(s) may be 201 bps INFO @ Fri, 10 Dec 2021 17:52:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.10_model.r WARNING @ Fri, 10 Dec 2021 17:52:59: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:52:59: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Fri, 10 Dec 2021 17:52:59: #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 17:52:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:52:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 17:53:03: 27000000 INFO @ Fri, 10 Dec 2021 17:53:11: 28000000 INFO @ Fri, 10 Dec 2021 17:53:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:53:19: 29000000 INFO @ Fri, 10 Dec 2021 17:53:25: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 17:53:25: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 17:53:25: #1 total tags in treatment: 10241091 INFO @ Fri, 10 Dec 2021 17:53:25: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 17:53:25: #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 17:53:25: #1 tags after filtering in treatment: 7331728 INFO @ Fri, 10 Dec 2021 17:53:25: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 17:53:25: #1 finished! INFO @ Fri, 10 Dec 2021 17:53:25: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 17:53:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 17:53:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.10_peaks.xls INFO @ Fri, 10 Dec 2021 17:53:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:53:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.10_summits.bed INFO @ Fri, 10 Dec 2021 17:53:25: Done! INFO @ Fri, 10 Dec 2021 17:53:25: #2 number of paired peaks: 3960 INFO @ Fri, 10 Dec 2021 17:53:25: start model_add_line... INFO @ Fri, 10 Dec 2021 17:53:26: start X-correlation... INFO @ Fri, 10 Dec 2021 17:53:26: end of X-cor INFO @ Fri, 10 Dec 2021 17:53:26: #2 finished! INFO @ Fri, 10 Dec 2021 17:53:26: #2 predicted fragment length is 201 bps INFO @ Fri, 10 Dec 2021 17:53:26: #2 alternative fragment length(s) may be 201 bps INFO @ Fri, 10 Dec 2021 17:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.20_model.r WARNING @ Fri, 10 Dec 2021 17:53:26: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 17:53:26: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Fri, 10 Dec 2021 17:53:26: #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 17:53:26: #3 Call peaks... INFO @ Fri, 10 Dec 2021 17:53:26: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7128 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 17:53:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 17:53:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.20_peaks.xls INFO @ Fri, 10 Dec 2021 17:53:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 17:53:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978729/ERX3978729.20_summits.bed INFO @ Fri, 10 Dec 2021 17:53:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3074 records, 4 fields): 4 millis CompletedMACS2peakCalling