Job ID = 14168383 SRX = ERX3978744 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17877385 spots for ERR3975754/ERR3975754.sra Written 17877385 spots for ERR3975754/ERR3975754.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169646 ("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: 00:37:00 17877385 reads; of these: 17877385 (100.00%) were paired; of these: 6690394 (37.42%) aligned concordantly 0 times 4543871 (25.42%) aligned concordantly exactly 1 time 6643120 (37.16%) aligned concordantly >1 times ---- 6690394 pairs aligned concordantly 0 times; of these: 1600749 (23.93%) aligned discordantly 1 time ---- 5089645 pairs aligned 0 times concordantly or discordantly; of these: 10179290 mates make up the pairs; of these: 6505662 (63.91%) aligned 0 times 303373 (2.98%) aligned exactly 1 time 3370255 (33.11%) aligned >1 times 81.80% overall alignment rate Time searching: 00:37:00 Overall time: 00:37:00 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 20 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] 4961931 / 12704349 = 0.3906 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 19:05:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.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 19:05:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:05:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:05:31: 1000000 INFO @ Fri, 10 Dec 2021 19:05:42: 2000000 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 19:05:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.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 19:05:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:05:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:05:52: 3000000 INFO @ Fri, 10 Dec 2021 19:06:01: 1000000 INFO @ Fri, 10 Dec 2021 19:06:04: 4000000 INFO @ Fri, 10 Dec 2021 19:06:11: 2000000 INFO @ Fri, 10 Dec 2021 19:06:16: 5000000 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 19:06:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.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 19:06:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:06:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:06:21: 3000000 INFO @ Fri, 10 Dec 2021 19:06:28: 6000000 INFO @ Fri, 10 Dec 2021 19:06:31: 1000000 INFO @ Fri, 10 Dec 2021 19:06:32: 4000000 INFO @ Fri, 10 Dec 2021 19:06:40: 7000000 INFO @ Fri, 10 Dec 2021 19:06:42: 2000000 INFO @ Fri, 10 Dec 2021 19:06:42: 5000000 INFO @ Fri, 10 Dec 2021 19:06:52: 8000000 INFO @ Fri, 10 Dec 2021 19:06:52: 3000000 INFO @ Fri, 10 Dec 2021 19:06:52: 6000000 INFO @ Fri, 10 Dec 2021 19:07:02: 4000000 INFO @ Fri, 10 Dec 2021 19:07:03: 7000000 INFO @ Fri, 10 Dec 2021 19:07:03: 9000000 INFO @ Fri, 10 Dec 2021 19:07:12: 5000000 INFO @ Fri, 10 Dec 2021 19:07:13: 8000000 INFO @ Fri, 10 Dec 2021 19:07:15: 10000000 INFO @ Fri, 10 Dec 2021 19:07:22: 6000000 INFO @ Fri, 10 Dec 2021 19:07:23: 9000000 INFO @ Fri, 10 Dec 2021 19:07:27: 11000000 INFO @ Fri, 10 Dec 2021 19:07:33: 7000000 INFO @ Fri, 10 Dec 2021 19:07:33: 10000000 INFO @ Fri, 10 Dec 2021 19:07:38: 12000000 INFO @ Fri, 10 Dec 2021 19:07:43: 8000000 INFO @ Fri, 10 Dec 2021 19:07:43: 11000000 INFO @ Fri, 10 Dec 2021 19:07:50: 13000000 INFO @ Fri, 10 Dec 2021 19:07:52: 9000000 INFO @ Fri, 10 Dec 2021 19:07:53: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:08:01: 14000000 INFO @ Fri, 10 Dec 2021 19:08:02: 13000000 INFO @ Fri, 10 Dec 2021 19:08:03: 10000000 INFO @ Fri, 10 Dec 2021 19:08:12: 15000000 INFO @ Fri, 10 Dec 2021 19:08:12: 14000000 INFO @ Fri, 10 Dec 2021 19:08:12: 11000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:08:22: 15000000 INFO @ Fri, 10 Dec 2021 19:08:22: 12000000 INFO @ Fri, 10 Dec 2021 19:08:23: 16000000 INFO @ Fri, 10 Dec 2021 19:08:31: 16000000 INFO @ Fri, 10 Dec 2021 19:08:32: 13000000 INFO @ Fri, 10 Dec 2021 19:08:35: 17000000 INFO @ Fri, 10 Dec 2021 19:08:41: 14000000 INFO @ Fri, 10 Dec 2021 19:08:41: 17000000 INFO @ Fri, 10 Dec 2021 19:08:47: 18000000 INFO @ Fri, 10 Dec 2021 19:08:50: 15000000 INFO @ Fri, 10 Dec 2021 19:08:52: 18000000 INFO @ Fri, 10 Dec 2021 19:08:59: 19000000 INFO @ Fri, 10 Dec 2021 19:09:00: 16000000 INFO @ Fri, 10 Dec 2021 19:09:02: 19000000 INFO @ Fri, 10 Dec 2021 19:09:03: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:09:03: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:09:03: #1 total tags in treatment: 6328136 INFO @ Fri, 10 Dec 2021 19:09:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:09:03: #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 19:09:03: #1 tags after filtering in treatment: 4530632 INFO @ Fri, 10 Dec 2021 19:09:03: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 19:09:03: #1 finished! INFO @ Fri, 10 Dec 2021 19:09:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:09:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:09:03: #2 number of paired peaks: 3310 INFO @ Fri, 10 Dec 2021 19:09:03: start model_add_line... INFO @ Fri, 10 Dec 2021 19:09:03: start X-correlation... INFO @ Fri, 10 Dec 2021 19:09:03: end of X-cor INFO @ Fri, 10 Dec 2021 19:09:03: #2 finished! INFO @ Fri, 10 Dec 2021 19:09:03: #2 predicted fragment length is 215 bps INFO @ Fri, 10 Dec 2021 19:09:03: #2 alternative fragment length(s) may be 215 bps INFO @ Fri, 10 Dec 2021 19:09:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.05_model.r WARNING @ Fri, 10 Dec 2021 19:09:03: #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 19:09:03: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Fri, 10 Dec 2021 19:09:03: #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 19:09:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:09:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:09:05: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:09:05: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:09:05: #1 total tags in treatment: 6328136 INFO @ Fri, 10 Dec 2021 19:09:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:09:05: #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 19:09:05: #1 tags after filtering in treatment: 4530632 INFO @ Fri, 10 Dec 2021 19:09:05: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 19:09:05: #1 finished! INFO @ Fri, 10 Dec 2021 19:09:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:09:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:09:06: #2 number of paired peaks: 3310 INFO @ Fri, 10 Dec 2021 19:09:06: start model_add_line... INFO @ Fri, 10 Dec 2021 19:09:06: start X-correlation... INFO @ Fri, 10 Dec 2021 19:09:06: end of X-cor INFO @ Fri, 10 Dec 2021 19:09:06: #2 finished! INFO @ Fri, 10 Dec 2021 19:09:06: #2 predicted fragment length is 215 bps INFO @ Fri, 10 Dec 2021 19:09:06: #2 alternative fragment length(s) may be 215 bps INFO @ Fri, 10 Dec 2021 19:09:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.10_model.r WARNING @ Fri, 10 Dec 2021 19:09:06: #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 19:09:06: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Fri, 10 Dec 2021 19:09:06: #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 19:09:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:09:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:09:09: 17000000 INFO @ Fri, 10 Dec 2021 19:09:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:09:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:09:16: 18000000 INFO @ Fri, 10 Dec 2021 19:09:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:09:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:09:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.05_summits.bed INFO @ Fri, 10 Dec 2021 19:09:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8810 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:09:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:09:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:09:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.10_summits.bed INFO @ Fri, 10 Dec 2021 19:09:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5091 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:09:23: 19000000 INFO @ Fri, 10 Dec 2021 19:09:26: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:09:26: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:09:26: #1 total tags in treatment: 6328136 INFO @ Fri, 10 Dec 2021 19:09:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:09:26: #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 19:09:26: #1 tags after filtering in treatment: 4530632 INFO @ Fri, 10 Dec 2021 19:09:26: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 19:09:26: #1 finished! INFO @ Fri, 10 Dec 2021 19:09:26: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:09:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:09:26: #2 number of paired peaks: 3310 INFO @ Fri, 10 Dec 2021 19:09:26: start model_add_line... INFO @ Fri, 10 Dec 2021 19:09:26: start X-correlation... INFO @ Fri, 10 Dec 2021 19:09:26: end of X-cor INFO @ Fri, 10 Dec 2021 19:09:26: #2 finished! INFO @ Fri, 10 Dec 2021 19:09:26: #2 predicted fragment length is 215 bps INFO @ Fri, 10 Dec 2021 19:09:26: #2 alternative fragment length(s) may be 215 bps INFO @ Fri, 10 Dec 2021 19:09:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.20_model.r WARNING @ Fri, 10 Dec 2021 19:09:26: #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 19:09:26: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Fri, 10 Dec 2021 19:09:26: #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 19:09:26: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:09:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:09:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:09:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:09:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:09:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978744/ERX3978744.20_summits.bed INFO @ Fri, 10 Dec 2021 19:09:42: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1796 records, 4 fields): 168 millis CompletedMACS2peakCalling