Job ID = 6627068 SRX = SRX8347283 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:44:02 prefetch.2.10.7: 1) Downloading 'SRR11795466'... 2020-07-14T00:44:02 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:49:50 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:49:50 prefetch.2.10.7: 1) 'SRR11795466' was downloaded successfully 2020-07-14T00:49:50 prefetch.2.10.7: 'SRR11795466' has 0 unresolved dependencies Read 14337940 spots for SRR11795466/SRR11795466.sra Written 14337940 spots for SRR11795466/SRR11795466.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627391 ("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: 00:36:53 14337940 reads; of these: 14337940 (100.00%) were paired; of these: 5154203 (35.95%) aligned concordantly 0 times 7663186 (53.45%) aligned concordantly exactly 1 time 1520551 (10.61%) aligned concordantly >1 times ---- 5154203 pairs aligned concordantly 0 times; of these: 676454 (13.12%) aligned discordantly 1 time ---- 4477749 pairs aligned 0 times concordantly or discordantly; of these: 8955498 mates make up the pairs; of these: 8404701 (93.85%) aligned 0 times 233735 (2.61%) aligned exactly 1 time 317062 (3.54%) aligned >1 times 70.69% overall alignment rate Time searching: 00:36:53 Overall time: 00:36:53 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 16 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] 3912817 / 9824238 = 0.3983 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:36:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.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 @ Tue, 14 Jul 2020 10:36:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:36:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:37:06: 1000000 INFO @ Tue, 14 Jul 2020 10:37:17: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:37:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.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 @ Tue, 14 Jul 2020 10:37:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:37:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:37:30: 3000000 INFO @ Tue, 14 Jul 2020 10:37:37: 1000000 INFO @ Tue, 14 Jul 2020 10:37:46: 4000000 INFO @ Tue, 14 Jul 2020 10:37:48: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:37:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.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 @ Tue, 14 Jul 2020 10:37:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:37:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:37:59: 3000000 INFO @ Tue, 14 Jul 2020 10:38:01: 5000000 INFO @ Tue, 14 Jul 2020 10:38:07: 1000000 INFO @ Tue, 14 Jul 2020 10:38:11: 4000000 INFO @ Tue, 14 Jul 2020 10:38:17: 6000000 INFO @ Tue, 14 Jul 2020 10:38:19: 2000000 INFO @ Tue, 14 Jul 2020 10:38:22: 5000000 INFO @ Tue, 14 Jul 2020 10:38:30: 3000000 INFO @ Tue, 14 Jul 2020 10:38:32: 7000000 INFO @ Tue, 14 Jul 2020 10:38:33: 6000000 INFO @ Tue, 14 Jul 2020 10:38:41: 4000000 INFO @ Tue, 14 Jul 2020 10:38:44: 7000000 INFO @ Tue, 14 Jul 2020 10:38:47: 8000000 INFO @ Tue, 14 Jul 2020 10:38:53: 5000000 INFO @ Tue, 14 Jul 2020 10:38:55: 8000000 INFO @ Tue, 14 Jul 2020 10:39:02: 9000000 INFO @ Tue, 14 Jul 2020 10:39:05: 6000000 INFO @ Tue, 14 Jul 2020 10:39:06: 9000000 INFO @ Tue, 14 Jul 2020 10:39:16: 7000000 INFO @ Tue, 14 Jul 2020 10:39:17: 10000000 INFO @ Tue, 14 Jul 2020 10:39:18: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:39:27: 8000000 INFO @ Tue, 14 Jul 2020 10:39:29: 11000000 INFO @ Tue, 14 Jul 2020 10:39:32: 11000000 INFO @ Tue, 14 Jul 2020 10:39:38: 9000000 INFO @ Tue, 14 Jul 2020 10:39:40: 12000000 INFO @ Tue, 14 Jul 2020 10:39:45: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:39:45: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:39:45: #1 total tags in treatment: 5425658 INFO @ Tue, 14 Jul 2020 10:39:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:39:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:39:45: #1 tags after filtering in treatment: 5291886 INFO @ Tue, 14 Jul 2020 10:39:45: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 14 Jul 2020 10:39:45: #1 finished! INFO @ Tue, 14 Jul 2020 10:39:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:39:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:39:45: #2 number of paired peaks: 344 WARNING @ Tue, 14 Jul 2020 10:39:45: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Tue, 14 Jul 2020 10:39:45: start model_add_line... INFO @ Tue, 14 Jul 2020 10:39:45: start X-correlation... INFO @ Tue, 14 Jul 2020 10:39:45: end of X-cor INFO @ Tue, 14 Jul 2020 10:39:45: #2 finished! INFO @ Tue, 14 Jul 2020 10:39:45: #2 predicted fragment length is 194 bps INFO @ Tue, 14 Jul 2020 10:39:45: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 14 Jul 2020 10:39:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.10_model.r WARNING @ Tue, 14 Jul 2020 10:39:45: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:39:45: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Tue, 14 Jul 2020 10:39:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:39:45: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:39:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:39:47: 12000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:39:49: 10000000 INFO @ Tue, 14 Jul 2020 10:39:54: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:39:54: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:39:54: #1 total tags in treatment: 5425658 INFO @ Tue, 14 Jul 2020 10:39:54: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:39:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:39:54: #1 tags after filtering in treatment: 5291886 INFO @ Tue, 14 Jul 2020 10:39:54: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 14 Jul 2020 10:39:54: #1 finished! INFO @ Tue, 14 Jul 2020 10:39:54: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:39:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:39:55: #2 number of paired peaks: 344 WARNING @ Tue, 14 Jul 2020 10:39:55: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Tue, 14 Jul 2020 10:39:55: start model_add_line... INFO @ Tue, 14 Jul 2020 10:39:55: start X-correlation... INFO @ Tue, 14 Jul 2020 10:39:55: end of X-cor INFO @ Tue, 14 Jul 2020 10:39:55: #2 finished! INFO @ Tue, 14 Jul 2020 10:39:55: #2 predicted fragment length is 194 bps INFO @ Tue, 14 Jul 2020 10:39:55: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 14 Jul 2020 10:39:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.05_model.r WARNING @ Tue, 14 Jul 2020 10:39:55: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:39:55: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Tue, 14 Jul 2020 10:39:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:39:55: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:39:59: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:40:00: 11000000 INFO @ Tue, 14 Jul 2020 10:40:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:40:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:40:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.10_summits.bed INFO @ Tue, 14 Jul 2020 10:40:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1462 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:40:09: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:40:10: 12000000 INFO @ Tue, 14 Jul 2020 10:40:15: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:40:15: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:40:15: #1 total tags in treatment: 5425658 INFO @ Tue, 14 Jul 2020 10:40:15: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:40:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:40:15: #1 tags after filtering in treatment: 5291886 INFO @ Tue, 14 Jul 2020 10:40:15: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 14 Jul 2020 10:40:15: #1 finished! INFO @ Tue, 14 Jul 2020 10:40:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:40:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:40:16: #2 number of paired peaks: 344 WARNING @ Tue, 14 Jul 2020 10:40:16: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Tue, 14 Jul 2020 10:40:16: start model_add_line... INFO @ Tue, 14 Jul 2020 10:40:16: start X-correlation... INFO @ Tue, 14 Jul 2020 10:40:16: end of X-cor INFO @ Tue, 14 Jul 2020 10:40:16: #2 finished! INFO @ Tue, 14 Jul 2020 10:40:16: #2 predicted fragment length is 194 bps INFO @ Tue, 14 Jul 2020 10:40:16: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 14 Jul 2020 10:40:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.20_model.r WARNING @ Tue, 14 Jul 2020 10:40:16: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:40:16: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Tue, 14 Jul 2020 10:40:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:40:16: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:40:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:40:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:40:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:40:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.05_summits.bed INFO @ Tue, 14 Jul 2020 10:40:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4313 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:40:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:40:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:40:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:40:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347283/SRX8347283.20_summits.bed INFO @ Tue, 14 Jul 2020 10:40:35: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 1 millis CompletedMACS2peakCalling