Job ID = 14167092 SRX = SRX7723694 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18383856 spots for SRR11084650/SRR11084650.sra Written 18383856 spots for SRR11084650/SRR11084650.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167511 ("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: 00:07:38 18383856 reads; of these: 18383856 (100.00%) were unpaired; of these: 1189267 (6.47%) aligned 0 times 11958998 (65.05%) aligned exactly 1 time 5235591 (28.48%) aligned >1 times 93.53% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 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 8 files... [bam_rmdupse_core] 2564518 / 17194589 = 0.1491 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 09:59:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.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 09:59:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:59:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:59:19: 1000000 INFO @ Fri, 10 Dec 2021 09:59:26: 2000000 INFO @ Fri, 10 Dec 2021 09:59:32: 3000000 INFO @ Fri, 10 Dec 2021 09:59:39: 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 09:59:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.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 09:59:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:59:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:59:46: 5000000 INFO @ Fri, 10 Dec 2021 09:59:50: 1000000 INFO @ Fri, 10 Dec 2021 09:59:53: 6000000 INFO @ Fri, 10 Dec 2021 09:59:57: 2000000 INFO @ Fri, 10 Dec 2021 10:00:00: 7000000 INFO @ Fri, 10 Dec 2021 10:00:05: 3000000 INFO @ Fri, 10 Dec 2021 10:00:08: 8000000 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 10:00:12: 4000000 INFO @ Fri, 10 Dec 2021 10:00:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.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 10:00:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:00:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:00:16: 9000000 INFO @ Fri, 10 Dec 2021 10:00:21: 5000000 INFO @ Fri, 10 Dec 2021 10:00:22: 1000000 INFO @ Fri, 10 Dec 2021 10:00:24: 10000000 INFO @ Fri, 10 Dec 2021 10:00:30: 6000000 INFO @ Fri, 10 Dec 2021 10:00:31: 2000000 INFO @ Fri, 10 Dec 2021 10:00:33: 11000000 INFO @ Fri, 10 Dec 2021 10:00:38: 7000000 INFO @ Fri, 10 Dec 2021 10:00:39: 3000000 INFO @ Fri, 10 Dec 2021 10:00:41: 12000000 INFO @ Fri, 10 Dec 2021 10:00:46: 8000000 INFO @ Fri, 10 Dec 2021 10:00:48: 4000000 INFO @ Fri, 10 Dec 2021 10:00:50: 13000000 INFO @ Fri, 10 Dec 2021 10:00:55: 9000000 INFO @ Fri, 10 Dec 2021 10:00:57: 5000000 INFO @ Fri, 10 Dec 2021 10:00:58: 14000000 INFO @ Fri, 10 Dec 2021 10:01:03: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:01:03: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:01:03: #1 total tags in treatment: 14630071 INFO @ Fri, 10 Dec 2021 10:01:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:01:03: #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 10:01:03: #1 tags after filtering in treatment: 14630071 INFO @ Fri, 10 Dec 2021 10:01:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:01:03: #1 finished! INFO @ Fri, 10 Dec 2021 10:01:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:01:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:01:03: 10000000 INFO @ Fri, 10 Dec 2021 10:01:04: #2 number of paired peaks: 1273 INFO @ Fri, 10 Dec 2021 10:01:04: start model_add_line... INFO @ Fri, 10 Dec 2021 10:01:05: start X-correlation... INFO @ Fri, 10 Dec 2021 10:01:05: end of X-cor INFO @ Fri, 10 Dec 2021 10:01:05: #2 finished! INFO @ Fri, 10 Dec 2021 10:01:05: #2 predicted fragment length is 69 bps INFO @ Fri, 10 Dec 2021 10:01:05: #2 alternative fragment length(s) may be 69 bps INFO @ Fri, 10 Dec 2021 10:01:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.05_model.r WARNING @ Fri, 10 Dec 2021 10:01:05: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:01:05: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Fri, 10 Dec 2021 10:01:05: #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 10:01:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:01:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:01:06: 6000000 INFO @ Fri, 10 Dec 2021 10:01:12: 11000000 INFO @ Fri, 10 Dec 2021 10:01:14: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:01:21: 12000000 INFO @ Fri, 10 Dec 2021 10:01:23: 8000000 INFO @ Fri, 10 Dec 2021 10:01:29: 13000000 INFO @ Fri, 10 Dec 2021 10:01:32: 9000000 INFO @ Fri, 10 Dec 2021 10:01:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:01:38: 14000000 INFO @ Fri, 10 Dec 2021 10:01:40: 10000000 INFO @ Fri, 10 Dec 2021 10:01:43: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:01:43: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:01:43: #1 total tags in treatment: 14630071 INFO @ Fri, 10 Dec 2021 10:01:43: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:01:43: #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 10:01:43: #1 tags after filtering in treatment: 14630071 INFO @ Fri, 10 Dec 2021 10:01:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:01:43: #1 finished! INFO @ Fri, 10 Dec 2021 10:01:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:01:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:01:44: #2 number of paired peaks: 1273 INFO @ Fri, 10 Dec 2021 10:01:44: start model_add_line... INFO @ Fri, 10 Dec 2021 10:01:44: start X-correlation... INFO @ Fri, 10 Dec 2021 10:01:44: end of X-cor INFO @ Fri, 10 Dec 2021 10:01:44: #2 finished! INFO @ Fri, 10 Dec 2021 10:01:44: #2 predicted fragment length is 69 bps INFO @ Fri, 10 Dec 2021 10:01:44: #2 alternative fragment length(s) may be 69 bps INFO @ Fri, 10 Dec 2021 10:01:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.10_model.r WARNING @ Fri, 10 Dec 2021 10:01:44: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:01:44: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Fri, 10 Dec 2021 10:01:44: #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 10:01:44: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:01:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:01:48: 11000000 INFO @ Fri, 10 Dec 2021 10:01:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:01:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:01:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.05_summits.bed INFO @ Fri, 10 Dec 2021 10:01:51: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (23407 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:01:56: 12000000 INFO @ Fri, 10 Dec 2021 10:02:04: 13000000 INFO @ Fri, 10 Dec 2021 10:02:12: 14000000 INFO @ Fri, 10 Dec 2021 10:02:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:02:17: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:02:17: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:02:17: #1 total tags in treatment: 14630071 INFO @ Fri, 10 Dec 2021 10:02:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:02:17: #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 10:02:17: #1 tags after filtering in treatment: 14630071 INFO @ Fri, 10 Dec 2021 10:02:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:02:17: #1 finished! INFO @ Fri, 10 Dec 2021 10:02:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:02:18: #2 number of paired peaks: 1273 INFO @ Fri, 10 Dec 2021 10:02:18: start model_add_line... INFO @ Fri, 10 Dec 2021 10:02:18: start X-correlation... INFO @ Fri, 10 Dec 2021 10:02:18: end of X-cor INFO @ Fri, 10 Dec 2021 10:02:18: #2 finished! INFO @ Fri, 10 Dec 2021 10:02:18: #2 predicted fragment length is 69 bps INFO @ Fri, 10 Dec 2021 10:02:18: #2 alternative fragment length(s) may be 69 bps INFO @ Fri, 10 Dec 2021 10:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.20_model.r WARNING @ Fri, 10 Dec 2021 10:02:18: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:02:18: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Fri, 10 Dec 2021 10:02:18: #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 10:02:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:02:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:02:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:02:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:02:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.10_summits.bed INFO @ Fri, 10 Dec 2021 10:02:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (9087 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:02:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:03:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:03:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:03:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723694/SRX7723694.20_summits.bed INFO @ Fri, 10 Dec 2021 10:03:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3231 records, 4 fields): 5 millis CompletedMACS2peakCalling