Job ID = 16439315 SRX = SRX15206493 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:52:32 prefetch.2.10.7: 1) Downloading 'SRR19139303'... 2022-08-02T05:52:32 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:52:40 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:52:40 prefetch.2.10.7: 'SRR19139303' is valid 2022-08-02T05:52:40 prefetch.2.10.7: 1) 'SRR19139303' was downloaded successfully 2022-08-02T05:52:40 prefetch.2.10.7: 'SRR19139303' has 0 unresolved dependencies Read 3850289 spots for SRR19139303/SRR19139303.sra Written 3850289 spots for SRR19139303/SRR19139303.sra 2022-08-02T05:52:55 prefetch.2.10.7: 1) Downloading 'SRR19139304'... 2022-08-02T05:52:55 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:53:05 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:53:05 prefetch.2.10.7: 'SRR19139304' is valid 2022-08-02T05:53:05 prefetch.2.10.7: 1) 'SRR19139304' was downloaded successfully 2022-08-02T05:53:05 prefetch.2.10.7: 'SRR19139304' has 0 unresolved dependencies Read 3850289 spots for SRR19139304/SRR19139304.sra Written 3850289 spots for SRR19139304/SRR19139304.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439354 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:26 7700578 reads; of these: 7700578 (100.00%) were unpaired; of these: 275671 (3.58%) aligned 0 times 6838707 (88.81%) aligned exactly 1 time 586200 (7.61%) aligned >1 times 96.42% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 1699421 / 7424907 = 0.2289 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 14:58:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.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 14:58:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:58:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:58:27: 1000000 INFO @ Tue, 02 Aug 2022 14:58:33: 2000000 INFO @ Tue, 02 Aug 2022 14:58:39: 3000000 INFO @ Tue, 02 Aug 2022 14:58:45: 4000000 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 14:58:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.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 14:58:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:58:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:58:52: 5000000 INFO @ Tue, 02 Aug 2022 14:58:57: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 14:58:57: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 14:58:57: #1 total tags in treatment: 5725486 INFO @ Tue, 02 Aug 2022 14:58:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:58:57: #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 14:58:57: 1000000 INFO @ Tue, 02 Aug 2022 14:58:57: #1 tags after filtering in treatment: 5725486 INFO @ Tue, 02 Aug 2022 14:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:58:57: #1 finished! INFO @ Tue, 02 Aug 2022 14:58:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:58:58: #2 number of paired peaks: 6823 INFO @ Tue, 02 Aug 2022 14:58:58: start model_add_line... INFO @ Tue, 02 Aug 2022 14:58:58: start X-correlation... INFO @ Tue, 02 Aug 2022 14:58:58: end of X-cor INFO @ Tue, 02 Aug 2022 14:58:58: #2 finished! INFO @ Tue, 02 Aug 2022 14:58:58: #2 predicted fragment length is 199 bps INFO @ Tue, 02 Aug 2022 14:58:58: #2 alternative fragment length(s) may be 199 bps INFO @ Tue, 02 Aug 2022 14:58:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.05_model.r INFO @ Tue, 02 Aug 2022 14:58:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:58:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:59:03: 2000000 INFO @ Tue, 02 Aug 2022 14:59:09: 3000000 INFO @ Tue, 02 Aug 2022 14:59:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:59:15: 4000000 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 14:59:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.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 14:59:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:59:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:59:21: 5000000 INFO @ Tue, 02 Aug 2022 14:59:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:59:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:59:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.05_summits.bed INFO @ Tue, 02 Aug 2022 14:59:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (7558 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:59:27: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 14:59:27: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 14:59:27: #1 total tags in treatment: 5725486 INFO @ Tue, 02 Aug 2022 14:59:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:59:27: #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 14:59:27: #1 tags after filtering in treatment: 5725486 INFO @ Tue, 02 Aug 2022 14:59:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:59:27: #1 finished! INFO @ Tue, 02 Aug 2022 14:59:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:59:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:59:27: #2 number of paired peaks: 6823 INFO @ Tue, 02 Aug 2022 14:59:27: start model_add_line... INFO @ Tue, 02 Aug 2022 14:59:27: 1000000 INFO @ Tue, 02 Aug 2022 14:59:27: start X-correlation... INFO @ Tue, 02 Aug 2022 14:59:27: end of X-cor INFO @ Tue, 02 Aug 2022 14:59:27: #2 finished! INFO @ Tue, 02 Aug 2022 14:59:27: #2 predicted fragment length is 199 bps INFO @ Tue, 02 Aug 2022 14:59:27: #2 alternative fragment length(s) may be 199 bps INFO @ Tue, 02 Aug 2022 14:59:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.10_model.r INFO @ Tue, 02 Aug 2022 14:59:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:59:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:59:35: 2000000 INFO @ Tue, 02 Aug 2022 14:59:42: 3000000 INFO @ Tue, 02 Aug 2022 14:59:43: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:59:49: 4000000 INFO @ Tue, 02 Aug 2022 14:59:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:59:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:59:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.10_summits.bed INFO @ Tue, 02 Aug 2022 14:59:51: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6061 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:59:56: 5000000 INFO @ Tue, 02 Aug 2022 15:00:02: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:00:02: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:00:02: #1 total tags in treatment: 5725486 INFO @ Tue, 02 Aug 2022 15:00:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:00:02: #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 15:00:02: #1 tags after filtering in treatment: 5725486 INFO @ Tue, 02 Aug 2022 15:00:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:00:02: #1 finished! INFO @ Tue, 02 Aug 2022 15:00:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:00:02: #2 number of paired peaks: 6823 INFO @ Tue, 02 Aug 2022 15:00:02: start model_add_line... INFO @ Tue, 02 Aug 2022 15:00:03: start X-correlation... INFO @ Tue, 02 Aug 2022 15:00:03: end of X-cor INFO @ Tue, 02 Aug 2022 15:00:03: #2 finished! INFO @ Tue, 02 Aug 2022 15:00:03: #2 predicted fragment length is 199 bps INFO @ Tue, 02 Aug 2022 15:00:03: #2 alternative fragment length(s) may be 199 bps INFO @ Tue, 02 Aug 2022 15:00:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.20_model.r INFO @ Tue, 02 Aug 2022 15:00:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:00:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:00:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:00:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:00:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:00:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206493/SRX15206493.20_summits.bed INFO @ Tue, 02 Aug 2022 15:00:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4409 records, 4 fields): 15 millis CompletedMACS2peakCalling