Job ID = 14168251 SRX = ERX3978725 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14040308 spots for ERR3975734/ERR3975734.sra Written 14040308 spots for ERR3975734/ERR3975734.sra Read 24317488 spots for ERR3975766/ERR3975766.sra Written 24317488 spots for ERR3975766/ERR3975766.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169474 ("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: 01:08:33 38357796 reads; of these: 38357796 (100.00%) were paired; of these: 13787062 (35.94%) aligned concordantly 0 times 2708512 (7.06%) aligned concordantly exactly 1 time 21862222 (57.00%) aligned concordantly >1 times ---- 13787062 pairs aligned concordantly 0 times; of these: 937017 (6.80%) aligned discordantly 1 time ---- 12850045 pairs aligned 0 times concordantly or discordantly; of these: 25700090 mates make up the pairs; of these: 11825252 (46.01%) aligned 0 times 412119 (1.60%) aligned exactly 1 time 13462719 (52.38%) aligned >1 times 84.59% overall alignment rate Time searching: 01:08:33 Overall time: 01:08:33 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 48 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] 19593824 / 25251245 = 0.7760 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 18:04:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.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 18:04:44: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:04:44: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:04:52: 1000000 INFO @ Fri, 10 Dec 2021 18:05:00: 2000000 INFO @ Fri, 10 Dec 2021 18:05:07: 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 18:05:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.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 18:05:14: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:05:14: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:05:15: 4000000 INFO @ Fri, 10 Dec 2021 18:05:22: 1000000 INFO @ Fri, 10 Dec 2021 18:05:23: 5000000 INFO @ Fri, 10 Dec 2021 18:05:30: 2000000 INFO @ Fri, 10 Dec 2021 18:05:31: 6000000 INFO @ Fri, 10 Dec 2021 18:05:39: 3000000 INFO @ Fri, 10 Dec 2021 18:05:39: 7000000 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 18:05:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.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 18:05:44: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:05:44: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:05:47: 8000000 INFO @ Fri, 10 Dec 2021 18:05:47: 4000000 INFO @ Fri, 10 Dec 2021 18:05:55: 9000000 INFO @ Fri, 10 Dec 2021 18:05:56: 1000000 INFO @ Fri, 10 Dec 2021 18:05:56: 5000000 INFO @ Fri, 10 Dec 2021 18:06:04: 10000000 INFO @ Fri, 10 Dec 2021 18:06:05: 6000000 INFO @ Fri, 10 Dec 2021 18:06:08: 2000000 INFO @ Fri, 10 Dec 2021 18:06:12: 11000000 INFO @ Fri, 10 Dec 2021 18:06:14: 7000000 INFO @ Fri, 10 Dec 2021 18:06:19: 3000000 INFO @ Fri, 10 Dec 2021 18:06:20: 12000000 INFO @ Fri, 10 Dec 2021 18:06:22: 8000000 INFO @ Fri, 10 Dec 2021 18:06:29: 13000000 INFO @ Fri, 10 Dec 2021 18:06:30: 4000000 INFO @ Fri, 10 Dec 2021 18:06:30: 9000000 INFO @ Fri, 10 Dec 2021 18:06:37: 14000000 INFO @ Fri, 10 Dec 2021 18:06:39: 10000000 INFO @ Fri, 10 Dec 2021 18:06:42: 5000000 INFO @ Fri, 10 Dec 2021 18:06:46: 15000000 INFO @ Fri, 10 Dec 2021 18:06:48: 11000000 INFO @ Fri, 10 Dec 2021 18:06:54: 16000000 INFO @ Fri, 10 Dec 2021 18:06:54: 6000000 INFO @ Fri, 10 Dec 2021 18:06:56: 12000000 INFO @ Fri, 10 Dec 2021 18:07:02: 17000000 INFO @ Fri, 10 Dec 2021 18:07:04: 13000000 INFO @ Fri, 10 Dec 2021 18:07:05: 7000000 INFO @ Fri, 10 Dec 2021 18:07:11: 18000000 INFO @ Fri, 10 Dec 2021 18:07:13: 14000000 INFO @ Fri, 10 Dec 2021 18:07:16: 8000000 INFO @ Fri, 10 Dec 2021 18:07:19: 19000000 INFO @ Fri, 10 Dec 2021 18:07:21: 15000000 INFO @ Fri, 10 Dec 2021 18:07:26: 9000000 INFO @ Fri, 10 Dec 2021 18:07:28: 20000000 INFO @ Fri, 10 Dec 2021 18:07:30: 16000000 INFO @ Fri, 10 Dec 2021 18:07:36: 21000000 INFO @ Fri, 10 Dec 2021 18:07:36: 10000000 INFO @ Fri, 10 Dec 2021 18:07:38: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:07:44: 22000000 INFO @ Fri, 10 Dec 2021 18:07:47: 18000000 INFO @ Fri, 10 Dec 2021 18:07:47: 11000000 INFO @ Fri, 10 Dec 2021 18:07:53: 23000000 INFO @ Fri, 10 Dec 2021 18:07:55: 19000000 INFO @ Fri, 10 Dec 2021 18:07:58: 12000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:08:02: 24000000 INFO @ Fri, 10 Dec 2021 18:08:04: 20000000 INFO @ Fri, 10 Dec 2021 18:08:09: 13000000 INFO @ Fri, 10 Dec 2021 18:08:11: 25000000 INFO @ Fri, 10 Dec 2021 18:08:12: 21000000 INFO @ Fri, 10 Dec 2021 18:08:17: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:08:17: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:08:17: #1 total tags in treatment: 5108940 INFO @ Fri, 10 Dec 2021 18:08:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:08:17: #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 18:08:17: #1 tags after filtering in treatment: 2887000 INFO @ Fri, 10 Dec 2021 18:08:17: #1 Redundant rate of treatment: 0.43 INFO @ Fri, 10 Dec 2021 18:08:17: #1 finished! INFO @ Fri, 10 Dec 2021 18:08:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:08:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:08:17: #2 number of paired peaks: 3696 INFO @ Fri, 10 Dec 2021 18:08:17: start model_add_line... INFO @ Fri, 10 Dec 2021 18:08:17: start X-correlation... INFO @ Fri, 10 Dec 2021 18:08:17: end of X-cor INFO @ Fri, 10 Dec 2021 18:08:17: #2 finished! INFO @ Fri, 10 Dec 2021 18:08:17: #2 predicted fragment length is 215 bps INFO @ Fri, 10 Dec 2021 18:08:17: #2 alternative fragment length(s) may be 215 bps INFO @ Fri, 10 Dec 2021 18:08:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.05_model.r WARNING @ Fri, 10 Dec 2021 18:08:17: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:08:17: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Fri, 10 Dec 2021 18:08:17: #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 18:08:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:08:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:08:20: 14000000 INFO @ Fri, 10 Dec 2021 18:08:20: 22000000 INFO @ Fri, 10 Dec 2021 18:08:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:08:28: 23000000 INFO @ Fri, 10 Dec 2021 18:08:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:08:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:08:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.05_summits.bed INFO @ Fri, 10 Dec 2021 18:08:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6425 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:08:30: 15000000 INFO @ Fri, 10 Dec 2021 18:08:36: 24000000 INFO @ Fri, 10 Dec 2021 18:08:40: 16000000 INFO @ Fri, 10 Dec 2021 18:08:45: 25000000 INFO @ Fri, 10 Dec 2021 18:08:51: 17000000 INFO @ Fri, 10 Dec 2021 18:08:51: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:08:51: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:08:51: #1 total tags in treatment: 5108940 INFO @ Fri, 10 Dec 2021 18:08:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:08:51: #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 18:08:51: #1 tags after filtering in treatment: 2887000 INFO @ Fri, 10 Dec 2021 18:08:51: #1 Redundant rate of treatment: 0.43 INFO @ Fri, 10 Dec 2021 18:08:51: #1 finished! INFO @ Fri, 10 Dec 2021 18:08:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:08:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:08:52: #2 number of paired peaks: 3696 INFO @ Fri, 10 Dec 2021 18:08:52: start model_add_line... INFO @ Fri, 10 Dec 2021 18:08:52: start X-correlation... INFO @ Fri, 10 Dec 2021 18:08:52: end of X-cor INFO @ Fri, 10 Dec 2021 18:08:52: #2 finished! INFO @ Fri, 10 Dec 2021 18:08:52: #2 predicted fragment length is 215 bps INFO @ Fri, 10 Dec 2021 18:08:52: #2 alternative fragment length(s) may be 215 bps INFO @ Fri, 10 Dec 2021 18:08:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.10_model.r WARNING @ Fri, 10 Dec 2021 18:08:52: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:08:52: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Fri, 10 Dec 2021 18:08:52: #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 18:08:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:08:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:09:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:09:01: 18000000 INFO @ Fri, 10 Dec 2021 18:09:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:09:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:09:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.10_summits.bed INFO @ Fri, 10 Dec 2021 18:09:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3108 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:09:11: 19000000 INFO @ Fri, 10 Dec 2021 18:09:21: 20000000 INFO @ Fri, 10 Dec 2021 18:09:31: 21000000 INFO @ Fri, 10 Dec 2021 18:09:40: 22000000 INFO @ Fri, 10 Dec 2021 18:09:49: 23000000 INFO @ Fri, 10 Dec 2021 18:09:58: 24000000 INFO @ Fri, 10 Dec 2021 18:10:08: 25000000 INFO @ Fri, 10 Dec 2021 18:10:15: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:10:15: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:10:15: #1 total tags in treatment: 5108940 INFO @ Fri, 10 Dec 2021 18:10:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:10:15: #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 18:10:15: #1 tags after filtering in treatment: 2887000 INFO @ Fri, 10 Dec 2021 18:10:15: #1 Redundant rate of treatment: 0.43 INFO @ Fri, 10 Dec 2021 18:10:15: #1 finished! INFO @ Fri, 10 Dec 2021 18:10:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:10:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:10:16: #2 number of paired peaks: 3696 INFO @ Fri, 10 Dec 2021 18:10:16: start model_add_line... INFO @ Fri, 10 Dec 2021 18:10:16: start X-correlation... INFO @ Fri, 10 Dec 2021 18:10:16: end of X-cor INFO @ Fri, 10 Dec 2021 18:10:16: #2 finished! INFO @ Fri, 10 Dec 2021 18:10:16: #2 predicted fragment length is 215 bps INFO @ Fri, 10 Dec 2021 18:10:16: #2 alternative fragment length(s) may be 215 bps INFO @ Fri, 10 Dec 2021 18:10:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.20_model.r WARNING @ Fri, 10 Dec 2021 18:10:16: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:10:16: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Fri, 10 Dec 2021 18:10:16: #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 18:10:16: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:10:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:10:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:10:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:10:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:10:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978725/ERX3978725.20_summits.bed INFO @ Fri, 10 Dec 2021 18:10:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (920 records, 4 fields): 3 millis CompletedMACS2peakCalling