Job ID = 14168317 SRX = ERX3978732 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26273849 spots for ERR3975741/ERR3975741.sra Written 26273849 spots for ERR3975741/ERR3975741.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169524 ("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: 00:48:06 26273849 reads; of these: 26273849 (100.00%) were paired; of these: 11256071 (42.84%) aligned concordantly 0 times 12569722 (47.84%) aligned concordantly exactly 1 time 2448056 (9.32%) aligned concordantly >1 times ---- 11256071 pairs aligned concordantly 0 times; of these: 3935854 (34.97%) aligned discordantly 1 time ---- 7320217 pairs aligned 0 times concordantly or discordantly; of these: 14640434 mates make up the pairs; of these: 12412691 (84.78%) aligned 0 times 740875 (5.06%) aligned exactly 1 time 1486868 (10.16%) aligned >1 times 76.38% overall alignment rate Time searching: 00:48:06 Overall time: 00:48:06 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 28 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1963250 / 18859261 = 0.1041 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 18:26:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.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 18:26:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:26:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:26:47: 1000000 INFO @ Fri, 10 Dec 2021 18:26:57: 2000000 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 18:27:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.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 18:27:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:27:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:27:07: 3000000 INFO @ Fri, 10 Dec 2021 18:27:17: 1000000 INFO @ Fri, 10 Dec 2021 18:27:18: 4000000 INFO @ Fri, 10 Dec 2021 18:27:27: 2000000 INFO @ Fri, 10 Dec 2021 18:27:30: 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 @ Fri, 10 Dec 2021 18:27:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.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 18:27:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:27:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:27:37: 3000000 INFO @ Fri, 10 Dec 2021 18:27:41: 6000000 INFO @ Fri, 10 Dec 2021 18:27:48: 4000000 INFO @ Fri, 10 Dec 2021 18:27:48: 1000000 INFO @ Fri, 10 Dec 2021 18:27:52: 7000000 INFO @ Fri, 10 Dec 2021 18:27:58: 5000000 INFO @ Fri, 10 Dec 2021 18:28:00: 2000000 INFO @ Fri, 10 Dec 2021 18:28:03: 8000000 INFO @ Fri, 10 Dec 2021 18:28:08: 6000000 INFO @ Fri, 10 Dec 2021 18:28:11: 3000000 INFO @ Fri, 10 Dec 2021 18:28:14: 9000000 INFO @ Fri, 10 Dec 2021 18:28:19: 7000000 INFO @ Fri, 10 Dec 2021 18:28:22: 4000000 INFO @ Fri, 10 Dec 2021 18:28:26: 10000000 INFO @ Fri, 10 Dec 2021 18:28:29: 8000000 INFO @ Fri, 10 Dec 2021 18:28:33: 5000000 INFO @ Fri, 10 Dec 2021 18:28:37: 11000000 INFO @ Fri, 10 Dec 2021 18:28:40: 9000000 INFO @ Fri, 10 Dec 2021 18:28:44: 6000000 INFO @ Fri, 10 Dec 2021 18:28:48: 12000000 INFO @ Fri, 10 Dec 2021 18:28:50: 10000000 INFO @ Fri, 10 Dec 2021 18:28:55: 7000000 INFO @ Fri, 10 Dec 2021 18:28:59: 13000000 INFO @ Fri, 10 Dec 2021 18:29:00: 11000000 INFO @ Fri, 10 Dec 2021 18:29:07: 8000000 INFO @ Fri, 10 Dec 2021 18:29:11: 12000000 INFO @ Fri, 10 Dec 2021 18:29:11: 14000000 INFO @ Fri, 10 Dec 2021 18:29:18: 9000000 INFO @ Fri, 10 Dec 2021 18:29:21: 13000000 INFO @ Fri, 10 Dec 2021 18:29:22: 15000000 INFO @ Fri, 10 Dec 2021 18:29:29: 10000000 INFO @ Fri, 10 Dec 2021 18:29:31: 14000000 INFO @ Fri, 10 Dec 2021 18:29:34: 16000000 INFO @ Fri, 10 Dec 2021 18:29:40: 11000000 INFO @ Fri, 10 Dec 2021 18:29:42: 15000000 INFO @ Fri, 10 Dec 2021 18:29:45: 17000000 INFO @ Fri, 10 Dec 2021 18:29:52: 12000000 INFO @ Fri, 10 Dec 2021 18:29:52: 16000000 INFO @ Fri, 10 Dec 2021 18:29:56: 18000000 INFO @ Fri, 10 Dec 2021 18:30:03: 17000000 INFO @ Fri, 10 Dec 2021 18:30:03: 13000000 INFO @ Fri, 10 Dec 2021 18:30:07: 19000000 INFO @ Fri, 10 Dec 2021 18:30:13: 18000000 INFO @ Fri, 10 Dec 2021 18:30:15: 14000000 INFO @ Fri, 10 Dec 2021 18:30:18: 20000000 INFO @ Fri, 10 Dec 2021 18:30:23: 19000000 INFO @ Fri, 10 Dec 2021 18:30:26: 15000000 INFO @ Fri, 10 Dec 2021 18:30:30: 21000000 INFO @ Fri, 10 Dec 2021 18:30:34: 20000000 INFO @ Fri, 10 Dec 2021 18:30:37: 16000000 INFO @ Fri, 10 Dec 2021 18:30:41: 22000000 INFO @ Fri, 10 Dec 2021 18:30:44: 21000000 INFO @ Fri, 10 Dec 2021 18:30:48: 17000000 INFO @ Fri, 10 Dec 2021 18:30:52: 23000000 INFO @ Fri, 10 Dec 2021 18:30:55: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:30:59: 18000000 INFO @ Fri, 10 Dec 2021 18:31:03: 24000000 INFO @ Fri, 10 Dec 2021 18:31:05: 23000000 INFO @ Fri, 10 Dec 2021 18:31:11: 19000000 INFO @ Fri, 10 Dec 2021 18:31:15: 25000000 INFO @ Fri, 10 Dec 2021 18:31:16: 24000000 INFO @ Fri, 10 Dec 2021 18:31:22: 20000000 INFO @ Fri, 10 Dec 2021 18:31:25: 26000000 INFO @ Fri, 10 Dec 2021 18:31:26: 25000000 INFO @ Fri, 10 Dec 2021 18:31:33: 21000000 INFO @ Fri, 10 Dec 2021 18:31:36: 27000000 INFO @ Fri, 10 Dec 2021 18:31:37: 26000000 INFO @ Fri, 10 Dec 2021 18:31:44: 22000000 INFO @ Fri, 10 Dec 2021 18:31:47: 28000000 INFO @ Fri, 10 Dec 2021 18:31:47: 27000000 INFO @ Fri, 10 Dec 2021 18:31:55: 23000000 INFO @ Fri, 10 Dec 2021 18:31:58: 28000000 INFO @ Fri, 10 Dec 2021 18:31:58: 29000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:32:06: 24000000 INFO @ Fri, 10 Dec 2021 18:32:08: 29000000 INFO @ Fri, 10 Dec 2021 18:32:09: 30000000 INFO @ Fri, 10 Dec 2021 18:32:17: 25000000 INFO @ Fri, 10 Dec 2021 18:32:18: 30000000 INFO @ Fri, 10 Dec 2021 18:32:20: 31000000 INFO @ Fri, 10 Dec 2021 18:32:28: 26000000 INFO @ Fri, 10 Dec 2021 18:32:29: 31000000 INFO @ Fri, 10 Dec 2021 18:32:31: 32000000 INFO @ Fri, 10 Dec 2021 18:32:39: 27000000 INFO @ Fri, 10 Dec 2021 18:32:39: 32000000 INFO @ Fri, 10 Dec 2021 18:32:42: 33000000 INFO @ Fri, 10 Dec 2021 18:32:50: 33000000 INFO @ Fri, 10 Dec 2021 18:32:50: 28000000 INFO @ Fri, 10 Dec 2021 18:32:53: 34000000 INFO @ Fri, 10 Dec 2021 18:33:00: 34000000 INFO @ Fri, 10 Dec 2021 18:33:01: 29000000 INFO @ Fri, 10 Dec 2021 18:33:05: 35000000 INFO @ Fri, 10 Dec 2021 18:33:10: 35000000 INFO @ Fri, 10 Dec 2021 18:33:12: 30000000 INFO @ Fri, 10 Dec 2021 18:33:16: 36000000 INFO @ Fri, 10 Dec 2021 18:33:18: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:33:18: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:33:18: #1 total tags in treatment: 13273115 INFO @ Fri, 10 Dec 2021 18:33:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:33:18: #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 18:33:19: #1 tags after filtering in treatment: 10693931 INFO @ Fri, 10 Dec 2021 18:33:19: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Dec 2021 18:33:19: #1 finished! INFO @ Fri, 10 Dec 2021 18:33:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:33:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:33:19: #2 number of paired peaks: 505 WARNING @ Fri, 10 Dec 2021 18:33:19: Fewer paired peaks (505) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 505 pairs to build model! INFO @ Fri, 10 Dec 2021 18:33:19: start model_add_line... INFO @ Fri, 10 Dec 2021 18:33:19: start X-correlation... INFO @ Fri, 10 Dec 2021 18:33:19: end of X-cor INFO @ Fri, 10 Dec 2021 18:33:19: #2 finished! INFO @ Fri, 10 Dec 2021 18:33:19: #2 predicted fragment length is 145 bps INFO @ Fri, 10 Dec 2021 18:33:19: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 10 Dec 2021 18:33:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.05_model.r WARNING @ Fri, 10 Dec 2021 18:33:19: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:33:19: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Fri, 10 Dec 2021 18:33:19: #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 18:33:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:33:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:33:21: 36000000 INFO @ Fri, 10 Dec 2021 18:33:23: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:33:23: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:33:23: #1 total tags in treatment: 13273115 INFO @ Fri, 10 Dec 2021 18:33:23: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:33:23: #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 18:33:23: #1 tags after filtering in treatment: 10693931 INFO @ Fri, 10 Dec 2021 18:33:23: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Dec 2021 18:33:23: #1 finished! INFO @ Fri, 10 Dec 2021 18:33:23: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:33:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:33:23: 31000000 INFO @ Fri, 10 Dec 2021 18:33:24: #2 number of paired peaks: 505 WARNING @ Fri, 10 Dec 2021 18:33:24: Fewer paired peaks (505) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 505 pairs to build model! INFO @ Fri, 10 Dec 2021 18:33:24: start model_add_line... INFO @ Fri, 10 Dec 2021 18:33:24: start X-correlation... INFO @ Fri, 10 Dec 2021 18:33:24: end of X-cor INFO @ Fri, 10 Dec 2021 18:33:24: #2 finished! INFO @ Fri, 10 Dec 2021 18:33:24: #2 predicted fragment length is 145 bps INFO @ Fri, 10 Dec 2021 18:33:24: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 10 Dec 2021 18:33:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.10_model.r WARNING @ Fri, 10 Dec 2021 18:33:24: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:33:24: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Fri, 10 Dec 2021 18:33:24: #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 18:33:24: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:33:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:33:33: 32000000 INFO @ Fri, 10 Dec 2021 18:33:43: 33000000 INFO @ Fri, 10 Dec 2021 18:33:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:33:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:33:52: 34000000 INFO @ Fri, 10 Dec 2021 18:33:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:33:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:33:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.05_summits.bed INFO @ Fri, 10 Dec 2021 18:33:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6598 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:34:02: 35000000 INFO @ Fri, 10 Dec 2021 18:34:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:34:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:34:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.10_summits.bed INFO @ Fri, 10 Dec 2021 18:34:05: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2711 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:34:12: 36000000 INFO @ Fri, 10 Dec 2021 18:34:14: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:34:14: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:34:14: #1 total tags in treatment: 13273115 INFO @ Fri, 10 Dec 2021 18:34:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:34:14: #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 18:34:14: #1 tags after filtering in treatment: 10693931 INFO @ Fri, 10 Dec 2021 18:34:14: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 10 Dec 2021 18:34:14: #1 finished! INFO @ Fri, 10 Dec 2021 18:34:14: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:34:15: #2 number of paired peaks: 505 WARNING @ Fri, 10 Dec 2021 18:34:15: Fewer paired peaks (505) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 505 pairs to build model! INFO @ Fri, 10 Dec 2021 18:34:15: start model_add_line... INFO @ Fri, 10 Dec 2021 18:34:15: start X-correlation... INFO @ Fri, 10 Dec 2021 18:34:15: end of X-cor INFO @ Fri, 10 Dec 2021 18:34:15: #2 finished! INFO @ Fri, 10 Dec 2021 18:34:15: #2 predicted fragment length is 145 bps INFO @ Fri, 10 Dec 2021 18:34:15: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 10 Dec 2021 18:34:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.20_model.r WARNING @ Fri, 10 Dec 2021 18:34:15: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:34:15: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Fri, 10 Dec 2021 18:34:15: #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 18:34:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:34:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:34:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:34:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:34:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:34:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978732/ERX3978732.20_summits.bed INFO @ Fri, 10 Dec 2021 18:34:53: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (578 records, 4 fields): 2 millis CompletedMACS2peakCalling