Job ID = 14172037 SRX = SRX9103802 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26652639 spots for SRR12621002/SRR12621002.sra Written 26652639 spots for SRR12621002/SRR12621002.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172622 ("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: 00:46:12 26652639 reads; of these: 26652639 (100.00%) were paired; of these: 6594472 (24.74%) aligned concordantly 0 times 11205848 (42.04%) aligned concordantly exactly 1 time 8852319 (33.21%) aligned concordantly >1 times ---- 6594472 pairs aligned concordantly 0 times; of these: 1960538 (29.73%) aligned discordantly 1 time ---- 4633934 pairs aligned 0 times concordantly or discordantly; of these: 9267868 mates make up the pairs; of these: 6895555 (74.40%) aligned 0 times 726476 (7.84%) aligned exactly 1 time 1645837 (17.76%) aligned >1 times 87.06% overall alignment rate Time searching: 00:46:13 Overall time: 00:46:13 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] 6814539 / 21747245 = 0.3134 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 14:56:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.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 14:56:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:56:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:57:02: 1000000 INFO @ Sat, 11 Dec 2021 14:57:11: 2000000 INFO @ Sat, 11 Dec 2021 14:57:19: 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 @ Sat, 11 Dec 2021 14:57:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.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 14:57:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:57:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:57:27: 4000000 INFO @ Sat, 11 Dec 2021 14:57:35: 5000000 INFO @ Sat, 11 Dec 2021 14:57:39: 1000000 INFO @ Sat, 11 Dec 2021 14:57:43: 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 @ Sat, 11 Dec 2021 14:57:51: 7000000 INFO @ Sat, 11 Dec 2021 14:57:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.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 14:57:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:57:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:57:57: 2000000 INFO @ Sat, 11 Dec 2021 14:58:00: 8000000 INFO @ Sat, 11 Dec 2021 14:58:01: 1000000 INFO @ Sat, 11 Dec 2021 14:58:08: 9000000 INFO @ Sat, 11 Dec 2021 14:58:09: 2000000 INFO @ Sat, 11 Dec 2021 14:58:17: 10000000 INFO @ Sat, 11 Dec 2021 14:58:17: 3000000 INFO @ Sat, 11 Dec 2021 14:58:18: 3000000 INFO @ Sat, 11 Dec 2021 14:58:26: 11000000 INFO @ Sat, 11 Dec 2021 14:58:26: 4000000 INFO @ Sat, 11 Dec 2021 14:58:33: 4000000 INFO @ Sat, 11 Dec 2021 14:58:35: 5000000 INFO @ Sat, 11 Dec 2021 14:58:36: 12000000 INFO @ Sat, 11 Dec 2021 14:58:44: 6000000 INFO @ Sat, 11 Dec 2021 14:58:46: 13000000 INFO @ Sat, 11 Dec 2021 14:58:48: 5000000 INFO @ Sat, 11 Dec 2021 14:58:54: 7000000 INFO @ Sat, 11 Dec 2021 14:58:55: 14000000 INFO @ Sat, 11 Dec 2021 14:59:03: 8000000 INFO @ Sat, 11 Dec 2021 14:59:05: 15000000 INFO @ Sat, 11 Dec 2021 14:59:05: 6000000 INFO @ Sat, 11 Dec 2021 14:59:12: 9000000 INFO @ Sat, 11 Dec 2021 14:59:14: 16000000 INFO @ Sat, 11 Dec 2021 14:59:22: 10000000 INFO @ Sat, 11 Dec 2021 14:59:23: 17000000 INFO @ Sat, 11 Dec 2021 14:59:24: 7000000 INFO @ Sat, 11 Dec 2021 14:59:33: 18000000 INFO @ Sat, 11 Dec 2021 14:59:33: 11000000 INFO @ Sat, 11 Dec 2021 14:59:43: 19000000 INFO @ Sat, 11 Dec 2021 14:59:43: 12000000 INFO @ Sat, 11 Dec 2021 14:59:43: 8000000 INFO @ Sat, 11 Dec 2021 14:59:53: 20000000 INFO @ Sat, 11 Dec 2021 14:59:53: 13000000 INFO @ Sat, 11 Dec 2021 15:00:02: 9000000 INFO @ Sat, 11 Dec 2021 15:00:03: 21000000 INFO @ Sat, 11 Dec 2021 15:00:03: 14000000 INFO @ Sat, 11 Dec 2021 15:00:11: 22000000 INFO @ Sat, 11 Dec 2021 15:00:12: 15000000 INFO @ Sat, 11 Dec 2021 15:00:19: 10000000 INFO @ Sat, 11 Dec 2021 15:00:21: 23000000 INFO @ Sat, 11 Dec 2021 15:00:21: 16000000 INFO @ Sat, 11 Dec 2021 15:00:31: 24000000 INFO @ Sat, 11 Dec 2021 15:00:32: 17000000 INFO @ Sat, 11 Dec 2021 15:00:38: 11000000 INFO @ Sat, 11 Dec 2021 15:00:40: 25000000 INFO @ Sat, 11 Dec 2021 15:00:41: 18000000 INFO @ Sat, 11 Dec 2021 15:00:49: 26000000 INFO @ Sat, 11 Dec 2021 15:00:50: 19000000 INFO @ Sat, 11 Dec 2021 15:00:55: 12000000 INFO @ Sat, 11 Dec 2021 15:00:58: 27000000 INFO @ Sat, 11 Dec 2021 15:01:00: 20000000 INFO @ Sat, 11 Dec 2021 15:01:06: 28000000 INFO @ Sat, 11 Dec 2021 15:01:08: 21000000 INFO @ Sat, 11 Dec 2021 15:01:13: 13000000 INFO @ Sat, 11 Dec 2021 15:01:15: 29000000 INFO @ Sat, 11 Dec 2021 15:01:17: 22000000 INFO @ Sat, 11 Dec 2021 15:01:24: 30000000 INFO @ Sat, 11 Dec 2021 15:01:25: 23000000 INFO @ Sat, 11 Dec 2021 15:01:30: 14000000 INFO @ Sat, 11 Dec 2021 15:01:33: 31000000 INFO @ Sat, 11 Dec 2021 15:01:34: 24000000 INFO @ Sat, 11 Dec 2021 15:01:42: 32000000 INFO @ Sat, 11 Dec 2021 15:01:42: 25000000 INFO @ Sat, 11 Dec 2021 15:01:46: 15000000 INFO @ Sat, 11 Dec 2021 15:01:48: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 15:01:48: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 15:01:48: #1 total tags in treatment: 13437315 INFO @ Sat, 11 Dec 2021 15:01:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:01:48: #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 15:01:49: #1 tags after filtering in treatment: 10466225 INFO @ Sat, 11 Dec 2021 15:01:49: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 11 Dec 2021 15:01:49: #1 finished! INFO @ Sat, 11 Dec 2021 15:01:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:01:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:01:50: #2 number of paired peaks: 392 WARNING @ Sat, 11 Dec 2021 15:01:50: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Sat, 11 Dec 2021 15:01:50: start model_add_line... INFO @ Sat, 11 Dec 2021 15:01:50: start X-correlation... INFO @ Sat, 11 Dec 2021 15:01:50: end of X-cor INFO @ Sat, 11 Dec 2021 15:01:50: #2 finished! INFO @ Sat, 11 Dec 2021 15:01:50: #2 predicted fragment length is 72 bps INFO @ Sat, 11 Dec 2021 15:01:50: #2 alternative fragment length(s) may be 62,72 bps INFO @ Sat, 11 Dec 2021 15:01:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.05_model.r WARNING @ Sat, 11 Dec 2021 15:01:50: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:01:50: #2 You may need to consider one of the other alternative d(s): 62,72 WARNING @ Sat, 11 Dec 2021 15:01:50: #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 15:01:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:01:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:01:51: 26000000 INFO @ Sat, 11 Dec 2021 15:01:59: 27000000 INFO @ Sat, 11 Dec 2021 15:02:04: 16000000 INFO @ Sat, 11 Dec 2021 15:02:07: 28000000 INFO @ Sat, 11 Dec 2021 15:02:16: 29000000 INFO @ Sat, 11 Dec 2021 15:02:20: 17000000 INFO @ Sat, 11 Dec 2021 15:02:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:02:24: 30000000 INFO @ Sat, 11 Dec 2021 15:02:32: 31000000 INFO @ Sat, 11 Dec 2021 15:02:39: 18000000 INFO @ Sat, 11 Dec 2021 15:02:41: 32000000 INFO @ Sat, 11 Dec 2021 15:02:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:02:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:02:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.05_summits.bed INFO @ Sat, 11 Dec 2021 15:02:41: Done! pass1 - making usageList (15 chroms): 13 millis pass2 - checking and writing primary data (7962 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:02:48: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 15:02:48: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 15:02:48: #1 total tags in treatment: 13437315 INFO @ Sat, 11 Dec 2021 15:02:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:02:48: #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 15:02:48: #1 tags after filtering in treatment: 10466225 INFO @ Sat, 11 Dec 2021 15:02:48: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 11 Dec 2021 15:02:48: #1 finished! INFO @ Sat, 11 Dec 2021 15:02:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:02:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:02:49: #2 number of paired peaks: 392 WARNING @ Sat, 11 Dec 2021 15:02:49: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Sat, 11 Dec 2021 15:02:49: start model_add_line... INFO @ Sat, 11 Dec 2021 15:02:50: start X-correlation... INFO @ Sat, 11 Dec 2021 15:02:50: end of X-cor INFO @ Sat, 11 Dec 2021 15:02:50: #2 finished! INFO @ Sat, 11 Dec 2021 15:02:50: #2 predicted fragment length is 72 bps INFO @ Sat, 11 Dec 2021 15:02:50: #2 alternative fragment length(s) may be 62,72 bps INFO @ Sat, 11 Dec 2021 15:02:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.20_model.r WARNING @ Sat, 11 Dec 2021 15:02:50: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:02:50: #2 You may need to consider one of the other alternative d(s): 62,72 WARNING @ Sat, 11 Dec 2021 15:02:50: #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 15:02:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:02:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:02:56: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:03:12: 20000000 INFO @ Sat, 11 Dec 2021 15:03:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:03:26: 21000000 INFO @ Sat, 11 Dec 2021 15:03:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:03:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:03:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.20_summits.bed INFO @ Sat, 11 Dec 2021 15:03:39: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (494 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:03:41: 22000000 INFO @ Sat, 11 Dec 2021 15:03:57: 23000000 INFO @ Sat, 11 Dec 2021 15:04:13: 24000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:04:30: 25000000 INFO @ Sat, 11 Dec 2021 15:04:48: 26000000 INFO @ Sat, 11 Dec 2021 15:05:05: 27000000 INFO @ Sat, 11 Dec 2021 15:05:22: 28000000 INFO @ Sat, 11 Dec 2021 15:05:41: 29000000 INFO @ Sat, 11 Dec 2021 15:05:58: 30000000 INFO @ Sat, 11 Dec 2021 15:06:16: 31000000 INFO @ Sat, 11 Dec 2021 15:06:35: 32000000 INFO @ Sat, 11 Dec 2021 15:06:50: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 15:06:50: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 15:06:50: #1 total tags in treatment: 13437315 INFO @ Sat, 11 Dec 2021 15:06:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:06:50: #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 15:06:50: #1 tags after filtering in treatment: 10466225 INFO @ Sat, 11 Dec 2021 15:06:50: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 11 Dec 2021 15:06:50: #1 finished! INFO @ Sat, 11 Dec 2021 15:06:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:06:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:06:51: #2 number of paired peaks: 392 WARNING @ Sat, 11 Dec 2021 15:06:51: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Sat, 11 Dec 2021 15:06:51: start model_add_line... INFO @ Sat, 11 Dec 2021 15:06:51: start X-correlation... INFO @ Sat, 11 Dec 2021 15:06:51: end of X-cor INFO @ Sat, 11 Dec 2021 15:06:51: #2 finished! INFO @ Sat, 11 Dec 2021 15:06:51: #2 predicted fragment length is 72 bps INFO @ Sat, 11 Dec 2021 15:06:51: #2 alternative fragment length(s) may be 62,72 bps INFO @ Sat, 11 Dec 2021 15:06:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.10_model.r WARNING @ Sat, 11 Dec 2021 15:06:52: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:06:52: #2 You may need to consider one of the other alternative d(s): 62,72 WARNING @ Sat, 11 Dec 2021 15:06:52: #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 15:06:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:06:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:07:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:07:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:07:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:07:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103802/SRX9103802.10_summits.bed INFO @ Sat, 11 Dec 2021 15:07:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3473 records, 4 fields): 11 millis CompletedMACS2peakCalling