Job ID = 14167078 SRX = SRX4712920 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23477454 spots for SRR7874050/SRR7874050.sra Written 23477454 spots for SRR7874050/SRR7874050.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167570 ("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: 00:38:50 23477454 reads; of these: 23477454 (100.00%) were paired; of these: 5321039 (22.66%) aligned concordantly 0 times 14909187 (63.50%) aligned concordantly exactly 1 time 3247228 (13.83%) aligned concordantly >1 times ---- 5321039 pairs aligned concordantly 0 times; of these: 1757157 (33.02%) aligned discordantly 1 time ---- 3563882 pairs aligned 0 times concordantly or discordantly; of these: 7127764 mates make up the pairs; of these: 5649371 (79.26%) aligned 0 times 597298 (8.38%) aligned exactly 1 time 881095 (12.36%) aligned >1 times 87.97% overall alignment rate Time searching: 00:38:50 Overall time: 00:38:50 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 20 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] 1842873 / 19771595 = 0.0932 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 10:30:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.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 10:30:42: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:30:42: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:30:52: 1000000 INFO @ Fri, 10 Dec 2021 10:31:01: 2000000 INFO @ Fri, 10 Dec 2021 10:31:10: 3000000 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 10:31:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.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 10:31:12: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:31:12: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:31:19: 1000000 INFO @ Fri, 10 Dec 2021 10:31:20: 4000000 INFO @ Fri, 10 Dec 2021 10:31:27: 2000000 INFO @ Fri, 10 Dec 2021 10:31:29: 5000000 INFO @ Fri, 10 Dec 2021 10:31:34: 3000000 INFO @ Fri, 10 Dec 2021 10:31:39: 6000000 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 10:31:41: 4000000 INFO @ Fri, 10 Dec 2021 10:31:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.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 10:31:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:31:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:31:49: 5000000 INFO @ Fri, 10 Dec 2021 10:31:49: 7000000 INFO @ Fri, 10 Dec 2021 10:31:53: 1000000 INFO @ Fri, 10 Dec 2021 10:31:56: 6000000 INFO @ Fri, 10 Dec 2021 10:31:59: 8000000 INFO @ Fri, 10 Dec 2021 10:32:02: 2000000 INFO @ Fri, 10 Dec 2021 10:32:03: 7000000 INFO @ Fri, 10 Dec 2021 10:32:09: 9000000 INFO @ Fri, 10 Dec 2021 10:32:11: 8000000 INFO @ Fri, 10 Dec 2021 10:32:12: 3000000 INFO @ Fri, 10 Dec 2021 10:32:19: 9000000 INFO @ Fri, 10 Dec 2021 10:32:20: 10000000 INFO @ Fri, 10 Dec 2021 10:32:23: 4000000 INFO @ Fri, 10 Dec 2021 10:32:26: 10000000 INFO @ Fri, 10 Dec 2021 10:32:30: 11000000 INFO @ Fri, 10 Dec 2021 10:32:33: 5000000 INFO @ Fri, 10 Dec 2021 10:32:34: 11000000 INFO @ Fri, 10 Dec 2021 10:32:41: 12000000 INFO @ Fri, 10 Dec 2021 10:32:41: 6000000 INFO @ Fri, 10 Dec 2021 10:32:42: 12000000 INFO @ Fri, 10 Dec 2021 10:32:49: 7000000 INFO @ Fri, 10 Dec 2021 10:32:50: 13000000 INFO @ Fri, 10 Dec 2021 10:32:52: 13000000 INFO @ Fri, 10 Dec 2021 10:32:58: 14000000 INFO @ Fri, 10 Dec 2021 10:33:00: 8000000 INFO @ Fri, 10 Dec 2021 10:33:03: 14000000 INFO @ Fri, 10 Dec 2021 10:33:05: 15000000 INFO @ Fri, 10 Dec 2021 10:33:10: 9000000 INFO @ Fri, 10 Dec 2021 10:33:13: 16000000 INFO @ Fri, 10 Dec 2021 10:33:13: 15000000 INFO @ Fri, 10 Dec 2021 10:33:20: 10000000 INFO @ Fri, 10 Dec 2021 10:33:21: 17000000 INFO @ Fri, 10 Dec 2021 10:33:24: 16000000 INFO @ Fri, 10 Dec 2021 10:33:28: 18000000 INFO @ Fri, 10 Dec 2021 10:33:29: 11000000 INFO @ Fri, 10 Dec 2021 10:33:34: 17000000 INFO @ Fri, 10 Dec 2021 10:33:36: 19000000 INFO @ Fri, 10 Dec 2021 10:33:39: 12000000 INFO @ Fri, 10 Dec 2021 10:33:44: 20000000 INFO @ Fri, 10 Dec 2021 10:33:45: 18000000 INFO @ Fri, 10 Dec 2021 10:33:49: 13000000 INFO @ Fri, 10 Dec 2021 10:33:51: 21000000 INFO @ Fri, 10 Dec 2021 10:33:55: 19000000 INFO @ Fri, 10 Dec 2021 10:33:59: 22000000 INFO @ Fri, 10 Dec 2021 10:33:59: 14000000 INFO @ Fri, 10 Dec 2021 10:34:05: 20000000 INFO @ Fri, 10 Dec 2021 10:34:07: 23000000 INFO @ Fri, 10 Dec 2021 10:34:09: 15000000 INFO @ Fri, 10 Dec 2021 10:34:15: 24000000 INFO @ Fri, 10 Dec 2021 10:34:16: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:34:19: 16000000 INFO @ Fri, 10 Dec 2021 10:34:22: 25000000 INFO @ Fri, 10 Dec 2021 10:34:26: 22000000 INFO @ Fri, 10 Dec 2021 10:34:29: 17000000 INFO @ Fri, 10 Dec 2021 10:34:30: 26000000 INFO @ Fri, 10 Dec 2021 10:34:36: 23000000 INFO @ Fri, 10 Dec 2021 10:34:37: 18000000 INFO @ Fri, 10 Dec 2021 10:34:38: 27000000 INFO @ Fri, 10 Dec 2021 10:34:45: 19000000 INFO @ Fri, 10 Dec 2021 10:34:45: 24000000 INFO @ Fri, 10 Dec 2021 10:34:46: 28000000 INFO @ Fri, 10 Dec 2021 10:34:52: 20000000 INFO @ Fri, 10 Dec 2021 10:34:53: 29000000 INFO @ Fri, 10 Dec 2021 10:34:55: 25000000 INFO @ Fri, 10 Dec 2021 10:35:00: 21000000 INFO @ Fri, 10 Dec 2021 10:35:01: 30000000 INFO @ Fri, 10 Dec 2021 10:35:05: 26000000 INFO @ Fri, 10 Dec 2021 10:35:08: 22000000 INFO @ Fri, 10 Dec 2021 10:35:09: 31000000 INFO @ Fri, 10 Dec 2021 10:35:14: 27000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:35:15: 23000000 INFO @ Fri, 10 Dec 2021 10:35:17: 32000000 INFO @ Fri, 10 Dec 2021 10:35:23: 24000000 INFO @ Fri, 10 Dec 2021 10:35:24: 28000000 INFO @ Fri, 10 Dec 2021 10:35:24: 33000000 INFO @ Fri, 10 Dec 2021 10:35:31: 25000000 INFO @ Fri, 10 Dec 2021 10:35:32: 34000000 INFO @ Fri, 10 Dec 2021 10:35:33: 29000000 INFO @ Fri, 10 Dec 2021 10:35:38: 26000000 INFO @ Fri, 10 Dec 2021 10:35:40: 35000000 INFO @ Fri, 10 Dec 2021 10:35:43: 30000000 INFO @ Fri, 10 Dec 2021 10:35:46: 27000000 INFO @ Fri, 10 Dec 2021 10:35:47: 36000000 INFO @ Fri, 10 Dec 2021 10:35:53: 31000000 INFO @ Fri, 10 Dec 2021 10:35:54: 28000000 INFO @ Fri, 10 Dec 2021 10:35:55: 37000000 INFO @ Fri, 10 Dec 2021 10:36:00: #1 tag size is determined as 76 bps INFO @ Fri, 10 Dec 2021 10:36:00: #1 tag size = 76 INFO @ Fri, 10 Dec 2021 10:36:00: #1 total tags in treatment: 16462126 INFO @ Fri, 10 Dec 2021 10:36:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:36:00: #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 10:36:00: #1 tags after filtering in treatment: 11949859 INFO @ Fri, 10 Dec 2021 10:36:00: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 10 Dec 2021 10:36:00: #1 finished! INFO @ Fri, 10 Dec 2021 10:36:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:36:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:36:01: #2 number of paired peaks: 557 WARNING @ Fri, 10 Dec 2021 10:36:01: Fewer paired peaks (557) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 557 pairs to build model! INFO @ Fri, 10 Dec 2021 10:36:01: start model_add_line... INFO @ Fri, 10 Dec 2021 10:36:01: start X-correlation... INFO @ Fri, 10 Dec 2021 10:36:01: end of X-cor INFO @ Fri, 10 Dec 2021 10:36:01: #2 finished! INFO @ Fri, 10 Dec 2021 10:36:01: #2 predicted fragment length is 122 bps INFO @ Fri, 10 Dec 2021 10:36:01: #2 alternative fragment length(s) may be 122 bps INFO @ Fri, 10 Dec 2021 10:36:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.10_model.r WARNING @ Fri, 10 Dec 2021 10:36:01: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:36:01: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Fri, 10 Dec 2021 10:36:01: #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 10:36:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:36:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:36:01: 29000000 INFO @ Fri, 10 Dec 2021 10:36:02: 32000000 INFO @ Fri, 10 Dec 2021 10:36:09: 30000000 INFO @ Fri, 10 Dec 2021 10:36:12: 33000000 INFO @ Fri, 10 Dec 2021 10:36:16: 31000000 INFO @ Fri, 10 Dec 2021 10:36:22: 34000000 INFO @ Fri, 10 Dec 2021 10:36:23: 32000000 INFO @ Fri, 10 Dec 2021 10:36:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:36:31: 33000000 INFO @ Fri, 10 Dec 2021 10:36:31: 35000000 INFO @ Fri, 10 Dec 2021 10:36:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:36:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:36:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.10_summits.bed INFO @ Fri, 10 Dec 2021 10:36:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7172 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:36:38: 34000000 INFO @ Fri, 10 Dec 2021 10:36:41: 36000000 INFO @ Fri, 10 Dec 2021 10:36:46: 35000000 INFO @ Fri, 10 Dec 2021 10:36:50: 37000000 INFO @ Fri, 10 Dec 2021 10:36:53: 36000000 INFO @ Fri, 10 Dec 2021 10:36:56: #1 tag size is determined as 76 bps INFO @ Fri, 10 Dec 2021 10:36:56: #1 tag size = 76 INFO @ Fri, 10 Dec 2021 10:36:56: #1 total tags in treatment: 16462126 INFO @ Fri, 10 Dec 2021 10:36:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:36:56: #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 10:36:57: #1 tags after filtering in treatment: 11949859 INFO @ Fri, 10 Dec 2021 10:36:57: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 10 Dec 2021 10:36:57: #1 finished! INFO @ Fri, 10 Dec 2021 10:36:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:36:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:36:58: #2 number of paired peaks: 557 WARNING @ Fri, 10 Dec 2021 10:36:58: Fewer paired peaks (557) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 557 pairs to build model! INFO @ Fri, 10 Dec 2021 10:36:58: start model_add_line... INFO @ Fri, 10 Dec 2021 10:36:58: start X-correlation... INFO @ Fri, 10 Dec 2021 10:36:58: end of X-cor INFO @ Fri, 10 Dec 2021 10:36:58: #2 finished! INFO @ Fri, 10 Dec 2021 10:36:58: #2 predicted fragment length is 122 bps INFO @ Fri, 10 Dec 2021 10:36:58: #2 alternative fragment length(s) may be 122 bps INFO @ Fri, 10 Dec 2021 10:36:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.05_model.r WARNING @ Fri, 10 Dec 2021 10:36:58: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:36:58: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Fri, 10 Dec 2021 10:36:58: #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 10:36:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:36:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:37:00: 37000000 INFO @ Fri, 10 Dec 2021 10:37:04: #1 tag size is determined as 76 bps INFO @ Fri, 10 Dec 2021 10:37:04: #1 tag size = 76 INFO @ Fri, 10 Dec 2021 10:37:04: #1 total tags in treatment: 16462126 INFO @ Fri, 10 Dec 2021 10:37:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:37:04: #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 10:37:04: #1 tags after filtering in treatment: 11949859 INFO @ Fri, 10 Dec 2021 10:37:04: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 10 Dec 2021 10:37:04: #1 finished! INFO @ Fri, 10 Dec 2021 10:37:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:37:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:37:05: #2 number of paired peaks: 557 WARNING @ Fri, 10 Dec 2021 10:37:05: Fewer paired peaks (557) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 557 pairs to build model! INFO @ Fri, 10 Dec 2021 10:37:05: start model_add_line... INFO @ Fri, 10 Dec 2021 10:37:05: start X-correlation... INFO @ Fri, 10 Dec 2021 10:37:05: end of X-cor INFO @ Fri, 10 Dec 2021 10:37:05: #2 finished! INFO @ Fri, 10 Dec 2021 10:37:05: #2 predicted fragment length is 122 bps INFO @ Fri, 10 Dec 2021 10:37:05: #2 alternative fragment length(s) may be 122 bps INFO @ Fri, 10 Dec 2021 10:37:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.20_model.r WARNING @ Fri, 10 Dec 2021 10:37:05: #2 Since the d (122) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:37:05: #2 You may need to consider one of the other alternative d(s): 122 WARNING @ Fri, 10 Dec 2021 10:37:05: #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 10:37:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:37:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:37:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:37:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:37:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:37:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:37:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.20_summits.bed INFO @ Fri, 10 Dec 2021 10:37:40: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1935 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:37:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:37:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:37:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712920/SRX4712920.05_summits.bed INFO @ Fri, 10 Dec 2021 10:37:42: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (14078 records, 4 fields): 17 millis CompletedMACS2peakCalling