Job ID = 14168325 SRX = ERX3978735 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24374378 spots for ERR3975744/ERR3975744.sra Written 24374378 spots for ERR3975744/ERR3975744.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169554 ("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: 00:51:21 24374378 reads; of these: 24374378 (100.00%) were paired; of these: 8573135 (35.17%) aligned concordantly 0 times 7404718 (30.38%) aligned concordantly exactly 1 time 8396525 (34.45%) aligned concordantly >1 times ---- 8573135 pairs aligned concordantly 0 times; of these: 2322542 (27.09%) aligned discordantly 1 time ---- 6250593 pairs aligned 0 times concordantly or discordantly; of these: 12501186 mates make up the pairs; of these: 7586584 (60.69%) aligned 0 times 434220 (3.47%) aligned exactly 1 time 4480382 (35.84%) aligned >1 times 84.44% overall alignment rate Time searching: 00:51:21 Overall time: 00:51:21 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] 6886572 / 18009772 = 0.3824 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 18:29:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.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 18:29:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:29:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:29:29: 1000000 INFO @ Fri, 10 Dec 2021 18:29:35: 2000000 INFO @ Fri, 10 Dec 2021 18:29:42: 3000000 INFO @ Fri, 10 Dec 2021 18:29:48: 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 18:29:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.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 18:29:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:29:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:29:55: 5000000 INFO @ Fri, 10 Dec 2021 18:30:02: 1000000 INFO @ Fri, 10 Dec 2021 18:30:03: 6000000 INFO @ Fri, 10 Dec 2021 18:30:11: 7000000 INFO @ Fri, 10 Dec 2021 18:30:11: 2000000 INFO @ Fri, 10 Dec 2021 18:30:19: 8000000 INFO @ Fri, 10 Dec 2021 18:30:20: 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 18:30:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.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 18:30:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:30:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:30:27: 9000000 INFO @ Fri, 10 Dec 2021 18:30:29: 4000000 INFO @ Fri, 10 Dec 2021 18:30:31: 1000000 INFO @ Fri, 10 Dec 2021 18:30:35: 10000000 INFO @ Fri, 10 Dec 2021 18:30:38: 5000000 INFO @ Fri, 10 Dec 2021 18:30:39: 2000000 INFO @ Fri, 10 Dec 2021 18:30:43: 11000000 INFO @ Fri, 10 Dec 2021 18:30:47: 3000000 INFO @ Fri, 10 Dec 2021 18:30:47: 6000000 INFO @ Fri, 10 Dec 2021 18:30:51: 12000000 INFO @ Fri, 10 Dec 2021 18:30:55: 4000000 INFO @ Fri, 10 Dec 2021 18:30:56: 7000000 INFO @ Fri, 10 Dec 2021 18:30:59: 13000000 INFO @ Fri, 10 Dec 2021 18:31:03: 5000000 INFO @ Fri, 10 Dec 2021 18:31:05: 8000000 INFO @ Fri, 10 Dec 2021 18:31:07: 14000000 INFO @ Fri, 10 Dec 2021 18:31:12: 6000000 INFO @ Fri, 10 Dec 2021 18:31:15: 9000000 INFO @ Fri, 10 Dec 2021 18:31:15: 15000000 INFO @ Fri, 10 Dec 2021 18:31:20: 7000000 INFO @ Fri, 10 Dec 2021 18:31:23: 16000000 INFO @ Fri, 10 Dec 2021 18:31:24: 10000000 INFO @ Fri, 10 Dec 2021 18:31:28: 8000000 INFO @ Fri, 10 Dec 2021 18:31:31: 17000000 INFO @ Fri, 10 Dec 2021 18:31:33: 11000000 INFO @ Fri, 10 Dec 2021 18:31:36: 9000000 INFO @ Fri, 10 Dec 2021 18:31:38: 18000000 INFO @ Fri, 10 Dec 2021 18:31:42: 12000000 INFO @ Fri, 10 Dec 2021 18:31:43: 10000000 INFO @ Fri, 10 Dec 2021 18:31:46: 19000000 INFO @ Fri, 10 Dec 2021 18:31:51: 13000000 INFO @ Fri, 10 Dec 2021 18:31:51: 11000000 INFO @ Fri, 10 Dec 2021 18:31:53: 20000000 INFO @ Fri, 10 Dec 2021 18:31:59: 12000000 INFO @ Fri, 10 Dec 2021 18:32:00: 14000000 INFO @ Fri, 10 Dec 2021 18:32:01: 21000000 INFO @ Fri, 10 Dec 2021 18:32:07: 13000000 INFO @ Fri, 10 Dec 2021 18:32:08: 22000000 INFO @ Fri, 10 Dec 2021 18:32:09: 15000000 INFO @ Fri, 10 Dec 2021 18:32:15: 14000000 INFO @ Fri, 10 Dec 2021 18:32:16: 23000000 INFO @ Fri, 10 Dec 2021 18:32:18: 16000000 INFO @ Fri, 10 Dec 2021 18:32:23: 15000000 INFO @ Fri, 10 Dec 2021 18:32:24: 24000000 INFO @ Fri, 10 Dec 2021 18:32:27: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:32:31: 16000000 INFO @ Fri, 10 Dec 2021 18:32:32: 25000000 INFO @ Fri, 10 Dec 2021 18:32:35: 18000000 INFO @ Fri, 10 Dec 2021 18:32:38: 17000000 INFO @ Fri, 10 Dec 2021 18:32:40: 26000000 INFO @ Fri, 10 Dec 2021 18:32:44: 19000000 INFO @ Fri, 10 Dec 2021 18:32:45: 18000000 INFO @ Fri, 10 Dec 2021 18:32:48: 27000000 INFO @ Fri, 10 Dec 2021 18:32:51: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:32:51: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:32:51: #1 total tags in treatment: 9115303 INFO @ Fri, 10 Dec 2021 18:32:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:32:51: #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 18:32:51: #1 tags after filtering in treatment: 6316078 INFO @ Fri, 10 Dec 2021 18:32:51: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 10 Dec 2021 18:32:51: #1 finished! INFO @ Fri, 10 Dec 2021 18:32:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:32:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:32:52: #2 number of paired peaks: 4693 INFO @ Fri, 10 Dec 2021 18:32:52: start model_add_line... INFO @ Fri, 10 Dec 2021 18:32:52: start X-correlation... INFO @ Fri, 10 Dec 2021 18:32:52: end of X-cor INFO @ Fri, 10 Dec 2021 18:32:52: #2 finished! INFO @ Fri, 10 Dec 2021 18:32:52: #2 predicted fragment length is 202 bps INFO @ Fri, 10 Dec 2021 18:32:52: #2 alternative fragment length(s) may be 202 bps INFO @ Fri, 10 Dec 2021 18:32:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.05_model.r WARNING @ Fri, 10 Dec 2021 18:32:52: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:32:52: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Fri, 10 Dec 2021 18:32:52: #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 18:32:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:32:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:32:53: 20000000 INFO @ Fri, 10 Dec 2021 18:32:53: 19000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:33:00: 20000000 INFO @ Fri, 10 Dec 2021 18:33:01: 21000000 INFO @ Fri, 10 Dec 2021 18:33:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:33:07: 21000000 INFO @ Fri, 10 Dec 2021 18:33:10: 22000000 INFO @ Fri, 10 Dec 2021 18:33:15: 22000000 INFO @ Fri, 10 Dec 2021 18:33:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:33:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:33:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.05_summits.bed INFO @ Fri, 10 Dec 2021 18:33:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11351 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:33:19: 23000000 INFO @ Fri, 10 Dec 2021 18:33:22: 23000000 INFO @ Fri, 10 Dec 2021 18:33:28: 24000000 INFO @ Fri, 10 Dec 2021 18:33:30: 24000000 INFO @ Fri, 10 Dec 2021 18:33:37: 25000000 INFO @ Fri, 10 Dec 2021 18:33:38: 25000000 INFO @ Fri, 10 Dec 2021 18:33:46: 26000000 INFO @ Fri, 10 Dec 2021 18:33:47: 26000000 INFO @ Fri, 10 Dec 2021 18:33:56: 27000000 INFO @ Fri, 10 Dec 2021 18:33:56: 27000000 INFO @ Fri, 10 Dec 2021 18:33:59: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:33:59: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:33:59: #1 total tags in treatment: 9115303 INFO @ Fri, 10 Dec 2021 18:33:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:33:59: #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 18:33:59: #1 tags after filtering in treatment: 6316078 INFO @ Fri, 10 Dec 2021 18:33:59: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 10 Dec 2021 18:33:59: #1 finished! INFO @ Fri, 10 Dec 2021 18:33:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:33:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:34:00: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:34:00: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:34:00: #1 total tags in treatment: 9115303 INFO @ Fri, 10 Dec 2021 18:34:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:34:00: #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 18:34:00: #1 tags after filtering in treatment: 6316078 INFO @ Fri, 10 Dec 2021 18:34:00: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 10 Dec 2021 18:34:00: #1 finished! INFO @ Fri, 10 Dec 2021 18:34:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:34:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:34:00: #2 number of paired peaks: 4693 INFO @ Fri, 10 Dec 2021 18:34:00: start model_add_line... INFO @ Fri, 10 Dec 2021 18:34:00: start X-correlation... INFO @ Fri, 10 Dec 2021 18:34:00: end of X-cor INFO @ Fri, 10 Dec 2021 18:34:00: #2 finished! INFO @ Fri, 10 Dec 2021 18:34:00: #2 predicted fragment length is 202 bps INFO @ Fri, 10 Dec 2021 18:34:00: #2 alternative fragment length(s) may be 202 bps INFO @ Fri, 10 Dec 2021 18:34:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.10_model.r WARNING @ Fri, 10 Dec 2021 18:34:00: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:34:00: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Fri, 10 Dec 2021 18:34:00: #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 18:34:00: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:34:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:34:01: #2 number of paired peaks: 4693 INFO @ Fri, 10 Dec 2021 18:34:01: start model_add_line... INFO @ Fri, 10 Dec 2021 18:34:01: start X-correlation... INFO @ Fri, 10 Dec 2021 18:34:01: end of X-cor INFO @ Fri, 10 Dec 2021 18:34:01: #2 finished! INFO @ Fri, 10 Dec 2021 18:34:01: #2 predicted fragment length is 202 bps INFO @ Fri, 10 Dec 2021 18:34:01: #2 alternative fragment length(s) may be 202 bps INFO @ Fri, 10 Dec 2021 18:34:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.20_model.r WARNING @ Fri, 10 Dec 2021 18:34:01: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:34:01: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Fri, 10 Dec 2021 18:34:01: #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 18:34:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:34:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:34:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:34:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:34:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:34:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:34:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.10_summits.bed INFO @ Fri, 10 Dec 2021 18:34:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7437 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:34:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:34:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:34:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978735/ERX3978735.20_summits.bed INFO @ Fri, 10 Dec 2021 18:34:24: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3241 records, 4 fields): 5 millis CompletedMACS2peakCalling