Job ID = 14171958 SRX = SRX9427716 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17450363 spots for SRR12975523/SRR12975523.sra Written 17450363 spots for SRR12975523/SRR12975523.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172449 ("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: 00:09:11 17450363 reads; of these: 17450363 (100.00%) were unpaired; of these: 314077 (1.80%) aligned 0 times 4596095 (26.34%) aligned exactly 1 time 12540191 (71.86%) aligned >1 times 98.20% overall alignment rate Time searching: 00:09:11 Overall time: 00:09:11 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] 4641668 / 17136286 = 0.2709 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 @ Sat, 11 Dec 2021 13:46:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.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 @ Sat, 11 Dec 2021 13:46:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:46:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:46:33: 1000000 INFO @ Sat, 11 Dec 2021 13:46:38: 2000000 INFO @ Sat, 11 Dec 2021 13:46:44: 3000000 INFO @ Sat, 11 Dec 2021 13:46:49: 4000000 INFO @ Sat, 11 Dec 2021 13:46:54: 5000000 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 @ Sat, 11 Dec 2021 13:46:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.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 @ Sat, 11 Dec 2021 13:46:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:46:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:46:59: 6000000 INFO @ Sat, 11 Dec 2021 13:47:03: 1000000 INFO @ Sat, 11 Dec 2021 13:47:05: 7000000 INFO @ Sat, 11 Dec 2021 13:47:08: 2000000 INFO @ Sat, 11 Dec 2021 13:47:10: 8000000 INFO @ Sat, 11 Dec 2021 13:47:13: 3000000 INFO @ Sat, 11 Dec 2021 13:47:16: 9000000 INFO @ Sat, 11 Dec 2021 13:47:17: 4000000 INFO @ Sat, 11 Dec 2021 13:47:21: 10000000 INFO @ Sat, 11 Dec 2021 13:47:22: 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 @ Sat, 11 Dec 2021 13:47:26: 11000000 INFO @ Sat, 11 Dec 2021 13:47:27: 6000000 INFO @ Sat, 11 Dec 2021 13:47:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.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 @ Sat, 11 Dec 2021 13:47:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:47:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:47:32: 12000000 INFO @ Sat, 11 Dec 2021 13:47:32: 7000000 INFO @ Sat, 11 Dec 2021 13:47:33: 1000000 INFO @ Sat, 11 Dec 2021 13:47:35: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:47:35: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:47:35: #1 total tags in treatment: 12494618 INFO @ Sat, 11 Dec 2021 13:47:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:47:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:47:35: #1 tags after filtering in treatment: 12494618 INFO @ Sat, 11 Dec 2021 13:47:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:47:35: #1 finished! INFO @ Sat, 11 Dec 2021 13:47:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:47:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:47:36: #2 number of paired peaks: 5950 INFO @ Sat, 11 Dec 2021 13:47:36: start model_add_line... INFO @ Sat, 11 Dec 2021 13:47:36: start X-correlation... INFO @ Sat, 11 Dec 2021 13:47:36: end of X-cor INFO @ Sat, 11 Dec 2021 13:47:36: #2 finished! INFO @ Sat, 11 Dec 2021 13:47:36: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 13:47:36: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sat, 11 Dec 2021 13:47:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.05_model.r WARNING @ Sat, 11 Dec 2021 13:47:36: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:47:36: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sat, 11 Dec 2021 13:47:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:47:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:47:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:47:38: 8000000 INFO @ Sat, 11 Dec 2021 13:47:39: 2000000 INFO @ Sat, 11 Dec 2021 13:47:43: 9000000 INFO @ Sat, 11 Dec 2021 13:47:44: 3000000 INFO @ Sat, 11 Dec 2021 13:47:48: 10000000 INFO @ Sat, 11 Dec 2021 13:47:49: 4000000 INFO @ Sat, 11 Dec 2021 13:47:53: 11000000 INFO @ Sat, 11 Dec 2021 13:47:55: 5000000 INFO @ Sat, 11 Dec 2021 13:47:58: 12000000 INFO @ Sat, 11 Dec 2021 13:48:00: 6000000 INFO @ Sat, 11 Dec 2021 13:48:00: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:48:00: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:48:00: #1 total tags in treatment: 12494618 INFO @ Sat, 11 Dec 2021 13:48:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:48:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:48:00: #1 tags after filtering in treatment: 12494618 INFO @ Sat, 11 Dec 2021 13:48:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:48:00: #1 finished! INFO @ Sat, 11 Dec 2021 13:48:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:48:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:48:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:48:02: #2 number of paired peaks: 5950 INFO @ Sat, 11 Dec 2021 13:48:02: start model_add_line... INFO @ Sat, 11 Dec 2021 13:48:02: start X-correlation... INFO @ Sat, 11 Dec 2021 13:48:02: end of X-cor INFO @ Sat, 11 Dec 2021 13:48:02: #2 finished! INFO @ Sat, 11 Dec 2021 13:48:02: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 13:48:02: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sat, 11 Dec 2021 13:48:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.10_model.r WARNING @ Sat, 11 Dec 2021 13:48:02: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:48:02: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sat, 11 Dec 2021 13:48:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:48:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:48:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:48:05: 7000000 INFO @ Sat, 11 Dec 2021 13:48:10: 8000000 INFO @ Sat, 11 Dec 2021 13:48:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:48:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:48:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.05_summits.bed INFO @ Sat, 11 Dec 2021 13:48:14: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (15309 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:48:16: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:48:21: 10000000 INFO @ Sat, 11 Dec 2021 13:48:26: 11000000 INFO @ Sat, 11 Dec 2021 13:48:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:48:31: 12000000 INFO @ Sat, 11 Dec 2021 13:48:34: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:48:34: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:48:34: #1 total tags in treatment: 12494618 INFO @ Sat, 11 Dec 2021 13:48:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:48:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:48:34: #1 tags after filtering in treatment: 12494618 INFO @ Sat, 11 Dec 2021 13:48:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:48:34: #1 finished! INFO @ Sat, 11 Dec 2021 13:48:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:48:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:48:35: #2 number of paired peaks: 5950 INFO @ Sat, 11 Dec 2021 13:48:35: start model_add_line... INFO @ Sat, 11 Dec 2021 13:48:36: start X-correlation... INFO @ Sat, 11 Dec 2021 13:48:36: end of X-cor INFO @ Sat, 11 Dec 2021 13:48:36: #2 finished! INFO @ Sat, 11 Dec 2021 13:48:36: #2 predicted fragment length is 55 bps INFO @ Sat, 11 Dec 2021 13:48:36: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sat, 11 Dec 2021 13:48:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.20_model.r WARNING @ Sat, 11 Dec 2021 13:48:36: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:48:36: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Sat, 11 Dec 2021 13:48:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:48:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:48:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:48:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:48:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:48:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.10_summits.bed INFO @ Sat, 11 Dec 2021 13:48:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9607 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:49:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:49:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:49:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:49:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427716/SRX9427716.20_summits.bed INFO @ Sat, 11 Dec 2021 13:49:14: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3353 records, 4 fields): 5 millis CompletedMACS2peakCalling