Job ID = 14168716 SRX = ERX3978769 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12730454 spots for ERR3975786/ERR3975786.sra Written 12730454 spots for ERR3975786/ERR3975786.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169844 ("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: 00:32:58 12730454 reads; of these: 12730454 (100.00%) were paired; of these: 5364658 (42.14%) aligned concordantly 0 times 2910806 (22.86%) aligned concordantly exactly 1 time 4454990 (34.99%) aligned concordantly >1 times ---- 5364658 pairs aligned concordantly 0 times; of these: 744914 (13.89%) aligned discordantly 1 time ---- 4619744 pairs aligned 0 times concordantly or discordantly; of these: 9239488 mates make up the pairs; of these: 5785694 (62.62%) aligned 0 times 203505 (2.20%) aligned exactly 1 time 3250289 (35.18%) aligned >1 times 77.28% overall alignment rate Time searching: 00:32:58 Overall time: 00:32:58 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 12 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] 3261366 / 8031032 = 0.4061 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 20:28:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.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 20:28:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:28:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:28:42: 1000000 INFO @ Fri, 10 Dec 2021 20:28:48: 2000000 INFO @ Fri, 10 Dec 2021 20:28:55: 3000000 INFO @ Fri, 10 Dec 2021 20:29:01: 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 20:29:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.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 20:29:06: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:29:06: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:29:07: 5000000 INFO @ Fri, 10 Dec 2021 20:29:14: 6000000 INFO @ Fri, 10 Dec 2021 20:29:15: 1000000 INFO @ Fri, 10 Dec 2021 20:29:21: 7000000 INFO @ Fri, 10 Dec 2021 20:29:24: 2000000 INFO @ Fri, 10 Dec 2021 20:29:27: 8000000 INFO @ Fri, 10 Dec 2021 20:29:33: 3000000 INFO @ Fri, 10 Dec 2021 20:29:34: 9000000 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 20:29:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.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 20:29:36: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:29:36: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:29:40: 10000000 INFO @ Fri, 10 Dec 2021 20:29:42: 4000000 INFO @ Fri, 10 Dec 2021 20:29:43: 1000000 INFO @ Fri, 10 Dec 2021 20:29:47: 11000000 INFO @ Fri, 10 Dec 2021 20:29:50: 2000000 INFO @ Fri, 10 Dec 2021 20:29:51: 5000000 INFO @ Fri, 10 Dec 2021 20:29:54: 12000000 INFO @ Fri, 10 Dec 2021 20:29:57: 3000000 INFO @ Fri, 10 Dec 2021 20:29:59: 6000000 INFO @ Fri, 10 Dec 2021 20:30:01: 13000000 INFO @ Fri, 10 Dec 2021 20:30:02: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:30:02: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:30:02: #1 total tags in treatment: 4184503 INFO @ Fri, 10 Dec 2021 20:30:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:30:02: #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 20:30:02: #1 tags after filtering in treatment: 2952679 INFO @ Fri, 10 Dec 2021 20:30:02: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Dec 2021 20:30:02: #1 finished! INFO @ Fri, 10 Dec 2021 20:30:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:30:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:30:02: #2 number of paired peaks: 5747 INFO @ Fri, 10 Dec 2021 20:30:02: start model_add_line... INFO @ Fri, 10 Dec 2021 20:30:02: start X-correlation... INFO @ Fri, 10 Dec 2021 20:30:02: end of X-cor INFO @ Fri, 10 Dec 2021 20:30:02: #2 finished! INFO @ Fri, 10 Dec 2021 20:30:02: #2 predicted fragment length is 197 bps INFO @ Fri, 10 Dec 2021 20:30:02: #2 alternative fragment length(s) may be 197 bps INFO @ Fri, 10 Dec 2021 20:30:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.05_model.r WARNING @ Fri, 10 Dec 2021 20:30:02: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:30:02: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Fri, 10 Dec 2021 20:30:02: #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 20:30:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:30:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:30:04: 4000000 INFO @ Fri, 10 Dec 2021 20:30:08: 7000000 INFO @ Fri, 10 Dec 2021 20:30:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:30:10: 5000000 INFO @ Fri, 10 Dec 2021 20:30:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:30:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:30:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.05_summits.bed INFO @ Fri, 10 Dec 2021 20:30:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9506 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:30:16: 8000000 INFO @ Fri, 10 Dec 2021 20:30:17: 6000000 INFO @ Fri, 10 Dec 2021 20:30:24: 7000000 INFO @ Fri, 10 Dec 2021 20:30:25: 9000000 INFO @ Fri, 10 Dec 2021 20:30:30: 8000000 INFO @ Fri, 10 Dec 2021 20:30:33: 10000000 INFO @ Fri, 10 Dec 2021 20:30:37: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:30:42: 11000000 INFO @ Fri, 10 Dec 2021 20:30:43: 10000000 INFO @ Fri, 10 Dec 2021 20:30:49: 11000000 INFO @ Fri, 10 Dec 2021 20:30:51: 12000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:30:56: 12000000 INFO @ Fri, 10 Dec 2021 20:31:00: 13000000 INFO @ Fri, 10 Dec 2021 20:31:02: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:31:02: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:31:02: #1 total tags in treatment: 4184503 INFO @ Fri, 10 Dec 2021 20:31:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:31:02: #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 20:31:02: #1 tags after filtering in treatment: 2952679 INFO @ Fri, 10 Dec 2021 20:31:02: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Dec 2021 20:31:02: #1 finished! INFO @ Fri, 10 Dec 2021 20:31:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:31:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:31:02: #2 number of paired peaks: 5747 INFO @ Fri, 10 Dec 2021 20:31:02: start model_add_line... INFO @ Fri, 10 Dec 2021 20:31:02: start X-correlation... INFO @ Fri, 10 Dec 2021 20:31:02: end of X-cor INFO @ Fri, 10 Dec 2021 20:31:02: #2 finished! INFO @ Fri, 10 Dec 2021 20:31:02: #2 predicted fragment length is 197 bps INFO @ Fri, 10 Dec 2021 20:31:02: #2 alternative fragment length(s) may be 197 bps INFO @ Fri, 10 Dec 2021 20:31:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.10_model.r WARNING @ Fri, 10 Dec 2021 20:31:02: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:31:02: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Fri, 10 Dec 2021 20:31:02: #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 20:31:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:31:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:31:03: 13000000 INFO @ Fri, 10 Dec 2021 20:31:04: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 20:31:04: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 20:31:04: #1 total tags in treatment: 4184503 INFO @ Fri, 10 Dec 2021 20:31:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:31:04: #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 20:31:04: #1 tags after filtering in treatment: 2952679 INFO @ Fri, 10 Dec 2021 20:31:04: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Dec 2021 20:31:04: #1 finished! INFO @ Fri, 10 Dec 2021 20:31:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:31:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:31:05: #2 number of paired peaks: 5747 INFO @ Fri, 10 Dec 2021 20:31:05: start model_add_line... INFO @ Fri, 10 Dec 2021 20:31:05: start X-correlation... INFO @ Fri, 10 Dec 2021 20:31:05: end of X-cor INFO @ Fri, 10 Dec 2021 20:31:05: #2 finished! INFO @ Fri, 10 Dec 2021 20:31:05: #2 predicted fragment length is 197 bps INFO @ Fri, 10 Dec 2021 20:31:05: #2 alternative fragment length(s) may be 197 bps INFO @ Fri, 10 Dec 2021 20:31:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.20_model.r WARNING @ Fri, 10 Dec 2021 20:31:05: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:31:05: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Fri, 10 Dec 2021 20:31:05: #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 20:31:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:31:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:31:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:31:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:31:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:31:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:31:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.20_summits.bed INFO @ Fri, 10 Dec 2021 20:31:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2063 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:31:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:31:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:31:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978769/ERX3978769.10_summits.bed INFO @ Fri, 10 Dec 2021 20:31:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5413 records, 4 fields): 6 millis CompletedMACS2peakCalling