Job ID = 16439316 SRX = SRX15206494 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:52:47 prefetch.2.10.7: 1) Downloading 'SRR19139301'... 2022-08-02T05:52:47 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:52:56 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:52:57 prefetch.2.10.7: 'SRR19139301' is valid 2022-08-02T05:52:57 prefetch.2.10.7: 1) 'SRR19139301' was downloaded successfully 2022-08-02T05:52:57 prefetch.2.10.7: 'SRR19139301' has 0 unresolved dependencies Read 3959468 spots for SRR19139301/SRR19139301.sra Written 3959468 spots for SRR19139301/SRR19139301.sra 2022-08-02T05:53:15 prefetch.2.10.7: 1) Downloading 'SRR19139302'... 2022-08-02T05:53:15 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:53:23 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:53:24 prefetch.2.10.7: 'SRR19139302' is valid 2022-08-02T05:53:24 prefetch.2.10.7: 1) 'SRR19139302' was downloaded successfully 2022-08-02T05:53:24 prefetch.2.10.7: 'SRR19139302' has 0 unresolved dependencies Read 3959468 spots for SRR19139302/SRR19139302.sra Written 3959468 spots for SRR19139302/SRR19139302.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439359 ("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: 00:02:54 7918936 reads; of these: 7918936 (100.00%) were unpaired; of these: 204061 (2.58%) aligned 0 times 6700949 (84.62%) aligned exactly 1 time 1013926 (12.80%) aligned >1 times 97.42% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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_rmdupse_core] 268531 / 7714875 = 0.0348 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:59:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.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, 02 Aug 2022 14:59:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:59:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:00:02: 1000000 INFO @ Tue, 02 Aug 2022 15:00:10: 2000000 INFO @ Tue, 02 Aug 2022 15:00:18: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:00:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.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, 02 Aug 2022 15:00:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:00:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:00:27: 4000000 INFO @ Tue, 02 Aug 2022 15:00:31: 1000000 INFO @ Tue, 02 Aug 2022 15:00:35: 5000000 INFO @ Tue, 02 Aug 2022 15:00:39: 2000000 INFO @ Tue, 02 Aug 2022 15:00:44: 6000000 INFO @ Tue, 02 Aug 2022 15:00:48: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:00:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.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, 02 Aug 2022 15:00:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:00:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:00:53: 7000000 INFO @ Tue, 02 Aug 2022 15:00:57: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:00:57: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:00:57: #1 total tags in treatment: 7446344 INFO @ Tue, 02 Aug 2022 15:00:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:00:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:00:57: #1 tags after filtering in treatment: 7446344 INFO @ Tue, 02 Aug 2022 15:00:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:00:57: #1 finished! INFO @ Tue, 02 Aug 2022 15:00:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:00:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:00:57: 4000000 INFO @ Tue, 02 Aug 2022 15:00:57: #2 number of paired peaks: 100 WARNING @ Tue, 02 Aug 2022 15:00:57: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Tue, 02 Aug 2022 15:00:57: start model_add_line... INFO @ Tue, 02 Aug 2022 15:00:57: start X-correlation... INFO @ Tue, 02 Aug 2022 15:00:57: end of X-cor INFO @ Tue, 02 Aug 2022 15:00:57: #2 finished! INFO @ Tue, 02 Aug 2022 15:00:57: #2 predicted fragment length is 199 bps INFO @ Tue, 02 Aug 2022 15:00:57: #2 alternative fragment length(s) may be 3,178,199,229 bps INFO @ Tue, 02 Aug 2022 15:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.05_model.r INFO @ Tue, 02 Aug 2022 15:00:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:01:02: 1000000 INFO @ Tue, 02 Aug 2022 15:01:06: 5000000 INFO @ Tue, 02 Aug 2022 15:01:11: 2000000 INFO @ Tue, 02 Aug 2022 15:01:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:01:14: 6000000 INFO @ Tue, 02 Aug 2022 15:01:19: 3000000 INFO @ Tue, 02 Aug 2022 15:01:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:01:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:01:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.05_summits.bed INFO @ Tue, 02 Aug 2022 15:01:21: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:01:23: 7000000 INFO @ Tue, 02 Aug 2022 15:01:26: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:01:26: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:01:26: #1 total tags in treatment: 7446344 INFO @ Tue, 02 Aug 2022 15:01:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:01:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:01:27: #1 tags after filtering in treatment: 7446344 INFO @ Tue, 02 Aug 2022 15:01:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:01:27: #1 finished! INFO @ Tue, 02 Aug 2022 15:01:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:01:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:01:27: #2 number of paired peaks: 100 WARNING @ Tue, 02 Aug 2022 15:01:27: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Tue, 02 Aug 2022 15:01:27: start model_add_line... INFO @ Tue, 02 Aug 2022 15:01:27: start X-correlation... INFO @ Tue, 02 Aug 2022 15:01:27: end of X-cor INFO @ Tue, 02 Aug 2022 15:01:27: #2 finished! INFO @ Tue, 02 Aug 2022 15:01:27: #2 predicted fragment length is 199 bps INFO @ Tue, 02 Aug 2022 15:01:27: #2 alternative fragment length(s) may be 3,178,199,229 bps INFO @ Tue, 02 Aug 2022 15:01:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.10_model.r INFO @ Tue, 02 Aug 2022 15:01:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:01:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:01:27: 4000000 INFO @ Tue, 02 Aug 2022 15:01:36: 5000000 INFO @ Tue, 02 Aug 2022 15:01:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:01:44: 6000000 INFO @ Tue, 02 Aug 2022 15:01:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:01:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:01:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.10_summits.bed INFO @ Tue, 02 Aug 2022 15:01:50: Done! pass1 - making usageList (7 chroms): 12 millis pass2 - checking and writing primary data (34 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:01:53: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:01:56: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:01:56: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:01:56: #1 total tags in treatment: 7446344 INFO @ Tue, 02 Aug 2022 15:01:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:01:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:01:56: #1 tags after filtering in treatment: 7446344 INFO @ Tue, 02 Aug 2022 15:01:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:01:56: #1 finished! INFO @ Tue, 02 Aug 2022 15:01:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:01:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:01:57: #2 number of paired peaks: 100 WARNING @ Tue, 02 Aug 2022 15:01:57: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Tue, 02 Aug 2022 15:01:57: start model_add_line... INFO @ Tue, 02 Aug 2022 15:01:57: start X-correlation... INFO @ Tue, 02 Aug 2022 15:01:57: end of X-cor INFO @ Tue, 02 Aug 2022 15:01:57: #2 finished! INFO @ Tue, 02 Aug 2022 15:01:57: #2 predicted fragment length is 199 bps INFO @ Tue, 02 Aug 2022 15:01:57: #2 alternative fragment length(s) may be 3,178,199,229 bps INFO @ Tue, 02 Aug 2022 15:01:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.20_model.r INFO @ Tue, 02 Aug 2022 15:01:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:01:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:02:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:02:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:02:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:02:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206494/SRX15206494.20_summits.bed INFO @ Tue, 02 Aug 2022 15:02:19: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (15 records, 4 fields): 13 millis CompletedMACS2peakCalling