Job ID = 6626637 SRX = SRX7262572 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 144021964 spots for SRR10582200/SRR10582200.sra Written 144021964 spots for SRR10582200/SRR10582200.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627024 ("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: 00:31:29 144021964 reads; of these: 144021964 (100.00%) were unpaired; of these: 91783250 (63.73%) aligned 0 times 40401915 (28.05%) aligned exactly 1 time 11836799 (8.22%) aligned >1 times 36.27% overall alignment rate Time searching: 00:31:29 Overall time: 00:31:29 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 24 files... [bam_rmdupse_core] 27183460 / 52238714 = 0.5204 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 08:57:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.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 08:57:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:57:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:57:43: 1000000 INFO @ Tue, 14 Jul 2020 08:57:50: 2000000 INFO @ Tue, 14 Jul 2020 08:57:56: 3000000 INFO @ Tue, 14 Jul 2020 08:58:02: 4000000 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 08:58:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.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 08:58:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:58:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:58:09: 5000000 INFO @ Tue, 14 Jul 2020 08:58:15: 1000000 INFO @ Tue, 14 Jul 2020 08:58:15: 6000000 INFO @ Tue, 14 Jul 2020 08:58:22: 7000000 INFO @ Tue, 14 Jul 2020 08:58:23: 2000000 INFO @ Tue, 14 Jul 2020 08:58:29: 8000000 INFO @ Tue, 14 Jul 2020 08:58:32: 3000000 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 08:58:36: 9000000 INFO @ Tue, 14 Jul 2020 08:58:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.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 08:58:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:58:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:58:41: 4000000 INFO @ Tue, 14 Jul 2020 08:58:43: 10000000 INFO @ Tue, 14 Jul 2020 08:58:44: 1000000 INFO @ Tue, 14 Jul 2020 08:58:49: 5000000 INFO @ Tue, 14 Jul 2020 08:58:50: 11000000 INFO @ Tue, 14 Jul 2020 08:58:51: 2000000 INFO @ Tue, 14 Jul 2020 08:58:57: 12000000 INFO @ Tue, 14 Jul 2020 08:58:57: 3000000 INFO @ Tue, 14 Jul 2020 08:58:58: 6000000 INFO @ Tue, 14 Jul 2020 08:59:04: 4000000 INFO @ Tue, 14 Jul 2020 08:59:04: 13000000 INFO @ Tue, 14 Jul 2020 08:59:07: 7000000 INFO @ Tue, 14 Jul 2020 08:59:11: 14000000 INFO @ Tue, 14 Jul 2020 08:59:12: 5000000 INFO @ Tue, 14 Jul 2020 08:59:17: 8000000 INFO @ Tue, 14 Jul 2020 08:59:18: 15000000 INFO @ Tue, 14 Jul 2020 08:59:19: 6000000 INFO @ Tue, 14 Jul 2020 08:59:24: 9000000 INFO @ Tue, 14 Jul 2020 08:59:25: 16000000 INFO @ Tue, 14 Jul 2020 08:59:26: 7000000 INFO @ Tue, 14 Jul 2020 08:59:31: 10000000 INFO @ Tue, 14 Jul 2020 08:59:32: 17000000 INFO @ Tue, 14 Jul 2020 08:59:33: 8000000 INFO @ Tue, 14 Jul 2020 08:59:37: 11000000 INFO @ Tue, 14 Jul 2020 08:59:39: 18000000 INFO @ Tue, 14 Jul 2020 08:59:40: 9000000 INFO @ Tue, 14 Jul 2020 08:59:43: 12000000 INFO @ Tue, 14 Jul 2020 08:59:45: 19000000 INFO @ Tue, 14 Jul 2020 08:59:47: 10000000 INFO @ Tue, 14 Jul 2020 08:59:50: 13000000 INFO @ Tue, 14 Jul 2020 08:59:52: 20000000 INFO @ Tue, 14 Jul 2020 08:59:54: 11000000 INFO @ Tue, 14 Jul 2020 08:59:56: 14000000 INFO @ Tue, 14 Jul 2020 08:59:59: 21000000 INFO @ Tue, 14 Jul 2020 09:00:01: 12000000 INFO @ Tue, 14 Jul 2020 09:00:02: 15000000 INFO @ Tue, 14 Jul 2020 09:00:06: 22000000 INFO @ Tue, 14 Jul 2020 09:00:08: 13000000 INFO @ Tue, 14 Jul 2020 09:00:09: 16000000 INFO @ Tue, 14 Jul 2020 09:00:12: 23000000 INFO @ Tue, 14 Jul 2020 09:00:15: 14000000 INFO @ Tue, 14 Jul 2020 09:00:15: 17000000 INFO @ Tue, 14 Jul 2020 09:00:19: 24000000 INFO @ Tue, 14 Jul 2020 09:00:21: 18000000 INFO @ Tue, 14 Jul 2020 09:00:22: 15000000 INFO @ Tue, 14 Jul 2020 09:00:25: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:00:26: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:00:26: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:00:26: #1 total tags in treatment: 25055254 INFO @ Tue, 14 Jul 2020 09:00:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:00:26: #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 09:00:26: #1 tags after filtering in treatment: 25055254 INFO @ Tue, 14 Jul 2020 09:00:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:00:26: #1 finished! INFO @ Tue, 14 Jul 2020 09:00:26: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:00:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:00:28: 19000000 INFO @ Tue, 14 Jul 2020 09:00:29: #2 number of paired peaks: 7764 INFO @ Tue, 14 Jul 2020 09:00:29: start model_add_line... INFO @ Tue, 14 Jul 2020 09:00:29: 16000000 INFO @ Tue, 14 Jul 2020 09:00:29: start X-correlation... INFO @ Tue, 14 Jul 2020 09:00:29: end of X-cor INFO @ Tue, 14 Jul 2020 09:00:29: #2 finished! INFO @ Tue, 14 Jul 2020 09:00:29: #2 predicted fragment length is 109 bps INFO @ Tue, 14 Jul 2020 09:00:29: #2 alternative fragment length(s) may be 4,109 bps INFO @ Tue, 14 Jul 2020 09:00:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.05_model.r WARNING @ Tue, 14 Jul 2020 09:00:29: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:00:29: #2 You may need to consider one of the other alternative d(s): 4,109 WARNING @ Tue, 14 Jul 2020 09:00:29: #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 09:00:29: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:00:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:00:34: 20000000 INFO @ Tue, 14 Jul 2020 09:00:36: 17000000 INFO @ Tue, 14 Jul 2020 09:00:40: 21000000 INFO @ Tue, 14 Jul 2020 09:00:43: 18000000 INFO @ Tue, 14 Jul 2020 09:00:46: 22000000 INFO @ Tue, 14 Jul 2020 09:00:49: 19000000 INFO @ Tue, 14 Jul 2020 09:00:52: 23000000 INFO @ Tue, 14 Jul 2020 09:00:56: 20000000 INFO @ Tue, 14 Jul 2020 09:00:58: 24000000 INFO @ Tue, 14 Jul 2020 09:01:02: 21000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:01:05: 25000000 INFO @ Tue, 14 Jul 2020 09:01:05: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:01:05: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:01:05: #1 total tags in treatment: 25055254 INFO @ Tue, 14 Jul 2020 09:01:05: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:01:05: #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 09:01:05: #1 tags after filtering in treatment: 25055254 INFO @ Tue, 14 Jul 2020 09:01:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:01:05: #1 finished! INFO @ Tue, 14 Jul 2020 09:01:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:01:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:01:08: #2 number of paired peaks: 7764 INFO @ Tue, 14 Jul 2020 09:01:08: start model_add_line... INFO @ Tue, 14 Jul 2020 09:01:08: start X-correlation... INFO @ Tue, 14 Jul 2020 09:01:08: end of X-cor INFO @ Tue, 14 Jul 2020 09:01:08: #2 finished! INFO @ Tue, 14 Jul 2020 09:01:08: #2 predicted fragment length is 109 bps INFO @ Tue, 14 Jul 2020 09:01:08: #2 alternative fragment length(s) may be 4,109 bps INFO @ Tue, 14 Jul 2020 09:01:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.10_model.r WARNING @ Tue, 14 Jul 2020 09:01:08: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:01:08: #2 You may need to consider one of the other alternative d(s): 4,109 WARNING @ Tue, 14 Jul 2020 09:01:08: #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 09:01:08: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:01:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:01:09: 22000000 INFO @ Tue, 14 Jul 2020 09:01:15: 23000000 INFO @ Tue, 14 Jul 2020 09:01:22: 24000000 INFO @ Tue, 14 Jul 2020 09:01:25: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:01:28: 25000000 INFO @ Tue, 14 Jul 2020 09:01:29: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:01:29: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:01:29: #1 total tags in treatment: 25055254 INFO @ Tue, 14 Jul 2020 09:01:29: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:01:29: #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 09:01:29: #1 tags after filtering in treatment: 25055254 INFO @ Tue, 14 Jul 2020 09:01:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:01:29: #1 finished! INFO @ Tue, 14 Jul 2020 09:01:29: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:01:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:01:31: #2 number of paired peaks: 7764 INFO @ Tue, 14 Jul 2020 09:01:31: start model_add_line... INFO @ Tue, 14 Jul 2020 09:01:32: start X-correlation... INFO @ Tue, 14 Jul 2020 09:01:32: end of X-cor INFO @ Tue, 14 Jul 2020 09:01:32: #2 finished! INFO @ Tue, 14 Jul 2020 09:01:32: #2 predicted fragment length is 109 bps INFO @ Tue, 14 Jul 2020 09:01:32: #2 alternative fragment length(s) may be 4,109 bps INFO @ Tue, 14 Jul 2020 09:01:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.20_model.r WARNING @ Tue, 14 Jul 2020 09:01:32: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:01:32: #2 You may need to consider one of the other alternative d(s): 4,109 WARNING @ Tue, 14 Jul 2020 09:01:32: #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 09:01:32: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:01:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:01:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:01:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:01:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.05_summits.bed INFO @ Tue, 14 Jul 2020 09:01:49: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12675 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:02:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:02:27: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.10_summits.bed INFO @ Tue, 14 Jul 2020 09:02:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9720 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:02:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:02:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:02:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262572/SRX7262572.20_summits.bed INFO @ Tue, 14 Jul 2020 09:02:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6039 records, 4 fields): 7 millis CompletedMACS2peakCalling