Job ID = 14168212 SRX = ERX3978956 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 36535125 spots for ERR3976027/ERR3976027.sra Written 36535125 spots for ERR3976027/ERR3976027.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169615 ("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: 02:30:01 36535125 reads; of these: 36535125 (100.00%) were paired; of these: 5203223 (14.24%) aligned concordantly 0 times 24365109 (66.69%) aligned concordantly exactly 1 time 6966793 (19.07%) aligned concordantly >1 times ---- 5203223 pairs aligned concordantly 0 times; of these: 1101921 (21.18%) aligned discordantly 1 time ---- 4101302 pairs aligned 0 times concordantly or discordantly; of these: 8202604 mates make up the pairs; of these: 4272869 (52.09%) aligned 0 times 1861941 (22.70%) aligned exactly 1 time 2067794 (25.21%) aligned >1 times 94.15% overall alignment rate Time searching: 02:30:01 Overall time: 02:30:01 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 32 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] 26016882 / 32214737 = 0.8076 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 19:00:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.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 19:00:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:00:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:00:12: 1000000 INFO @ Fri, 10 Dec 2021 19:00:19: 2000000 INFO @ Fri, 10 Dec 2021 19:00:26: 3000000 INFO @ Fri, 10 Dec 2021 19:00:33: 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 19:00:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.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 19:00:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:00:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:00:41: 5000000 INFO @ Fri, 10 Dec 2021 19:00:43: 1000000 INFO @ Fri, 10 Dec 2021 19:00:48: 6000000 INFO @ Fri, 10 Dec 2021 19:00:51: 2000000 INFO @ Fri, 10 Dec 2021 19:00:56: 7000000 INFO @ Fri, 10 Dec 2021 19:00:59: 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 19:01:04: 8000000 INFO @ Fri, 10 Dec 2021 19:01:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.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 19:01:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:01:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:01:07: 4000000 INFO @ Fri, 10 Dec 2021 19:01:12: 9000000 INFO @ Fri, 10 Dec 2021 19:01:14: 1000000 INFO @ Fri, 10 Dec 2021 19:01:16: 5000000 INFO @ Fri, 10 Dec 2021 19:01:21: 10000000 INFO @ Fri, 10 Dec 2021 19:01:22: 2000000 INFO @ Fri, 10 Dec 2021 19:01:24: 6000000 INFO @ Fri, 10 Dec 2021 19:01:29: 11000000 INFO @ Fri, 10 Dec 2021 19:01:30: 3000000 INFO @ Fri, 10 Dec 2021 19:01:32: 7000000 INFO @ Fri, 10 Dec 2021 19:01:38: 4000000 INFO @ Fri, 10 Dec 2021 19:01:38: 12000000 INFO @ Fri, 10 Dec 2021 19:01:40: 8000000 INFO @ Fri, 10 Dec 2021 19:01:45: 5000000 INFO @ Fri, 10 Dec 2021 19:01:46: 13000000 INFO @ Fri, 10 Dec 2021 19:01:49: 9000000 INFO @ Fri, 10 Dec 2021 19:01:53: 6000000 INFO @ Fri, 10 Dec 2021 19:01:54: 14000000 INFO @ Fri, 10 Dec 2021 19:01:57: 10000000 INFO @ Fri, 10 Dec 2021 19:02:01: 7000000 INFO @ Fri, 10 Dec 2021 19:02:03: 15000000 INFO @ Fri, 10 Dec 2021 19:02:06: 11000000 INFO @ Fri, 10 Dec 2021 19:02:09: 8000000 INFO @ Fri, 10 Dec 2021 19:02:11: 16000000 INFO @ Fri, 10 Dec 2021 19:02:14: 12000000 INFO @ Fri, 10 Dec 2021 19:02:16: 9000000 INFO @ Fri, 10 Dec 2021 19:02:17: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:02:17: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:02:17: #1 total tags in treatment: 6169844 INFO @ Fri, 10 Dec 2021 19:02:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:02:17: #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 19:02:17: #1 tags after filtering in treatment: 5409363 INFO @ Fri, 10 Dec 2021 19:02:17: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 19:02:17: #1 finished! INFO @ Fri, 10 Dec 2021 19:02:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:02:18: #2 number of paired peaks: 3362 INFO @ Fri, 10 Dec 2021 19:02:18: start model_add_line... INFO @ Fri, 10 Dec 2021 19:02:18: start X-correlation... INFO @ Fri, 10 Dec 2021 19:02:18: end of X-cor INFO @ Fri, 10 Dec 2021 19:02:18: #2 finished! INFO @ Fri, 10 Dec 2021 19:02:18: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 19:02:18: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 19:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.05_model.r WARNING @ Fri, 10 Dec 2021 19:02:18: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:02:18: #2 You may need to consider one of the other alternative d(s): 155 WARNING @ Fri, 10 Dec 2021 19:02:18: #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 19:02:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:02:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:02:22: 13000000 INFO @ Fri, 10 Dec 2021 19:02:24: 10000000 INFO @ Fri, 10 Dec 2021 19:02:30: 14000000 INFO @ Fri, 10 Dec 2021 19:02:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:02:32: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:02:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:02:39: 15000000 INFO @ Fri, 10 Dec 2021 19:02:39: 12000000 INFO @ Fri, 10 Dec 2021 19:02:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:02:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.05_summits.bed INFO @ Fri, 10 Dec 2021 19:02:39: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11326 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:02:46: 13000000 INFO @ Fri, 10 Dec 2021 19:02:47: 16000000 INFO @ Fri, 10 Dec 2021 19:02:53: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:02:53: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:02:53: #1 total tags in treatment: 6169844 INFO @ Fri, 10 Dec 2021 19:02:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:02:53: #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 19:02:53: #1 tags after filtering in treatment: 5409363 INFO @ Fri, 10 Dec 2021 19:02:53: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 19:02:53: #1 finished! INFO @ Fri, 10 Dec 2021 19:02:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:02:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:02:54: #2 number of paired peaks: 3362 INFO @ Fri, 10 Dec 2021 19:02:54: start model_add_line... INFO @ Fri, 10 Dec 2021 19:02:54: start X-correlation... INFO @ Fri, 10 Dec 2021 19:02:54: end of X-cor INFO @ Fri, 10 Dec 2021 19:02:54: #2 finished! INFO @ Fri, 10 Dec 2021 19:02:54: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 19:02:54: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 19:02:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.10_model.r WARNING @ Fri, 10 Dec 2021 19:02:54: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:02:54: #2 You may need to consider one of the other alternative d(s): 155 WARNING @ Fri, 10 Dec 2021 19:02:54: #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 19:02:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:02:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:02:54: 14000000 INFO @ Fri, 10 Dec 2021 19:03:02: 15000000 INFO @ Fri, 10 Dec 2021 19:03:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:03:09: 16000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:03:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:03:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:03:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.10_summits.bed INFO @ Fri, 10 Dec 2021 19:03:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7455 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:03:15: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 19:03:15: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 19:03:15: #1 total tags in treatment: 6169844 INFO @ Fri, 10 Dec 2021 19:03:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:03:15: #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 19:03:15: #1 tags after filtering in treatment: 5409363 INFO @ Fri, 10 Dec 2021 19:03:15: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 10 Dec 2021 19:03:15: #1 finished! INFO @ Fri, 10 Dec 2021 19:03:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:03:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:03:16: #2 number of paired peaks: 3362 INFO @ Fri, 10 Dec 2021 19:03:16: start model_add_line... INFO @ Fri, 10 Dec 2021 19:03:16: start X-correlation... INFO @ Fri, 10 Dec 2021 19:03:16: end of X-cor INFO @ Fri, 10 Dec 2021 19:03:16: #2 finished! INFO @ Fri, 10 Dec 2021 19:03:16: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 19:03:16: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 19:03:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.20_model.r WARNING @ Fri, 10 Dec 2021 19:03:16: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:03:16: #2 You may need to consider one of the other alternative d(s): 155 WARNING @ Fri, 10 Dec 2021 19:03:16: #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 19:03:16: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:03:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:03:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:03:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:03:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:03:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978956/ERX3978956.20_summits.bed INFO @ Fri, 10 Dec 2021 19:03:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3339 records, 4 fields): 6 millis CompletedMACS2peakCalling