Job ID = 12266651 SRX = SRX7806723 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 33767508 spots for SRR11186389/SRR11186389.sra Written 33767508 spots for SRR11186389/SRR11186389.sra fastq に変換しました。 bowtie でマッピング中... Your job 12267990 ("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: 01:12:52 33767508 reads; of these: 33767508 (100.00%) were paired; of these: 17032671 (50.44%) aligned concordantly 0 times 10947606 (32.42%) aligned concordantly exactly 1 time 5787231 (17.14%) aligned concordantly >1 times ---- 17032671 pairs aligned concordantly 0 times; of these: 2949288 (17.32%) aligned discordantly 1 time ---- 14083383 pairs aligned 0 times concordantly or discordantly; of these: 28166766 mates make up the pairs; of these: 23422954 (83.16%) aligned 0 times 2441429 (8.67%) aligned exactly 1 time 2302383 (8.17%) aligned >1 times 65.32% overall alignment rate Time searching: 01:12:52 Overall time: 01:12:52 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] 5527699 / 19582425 = 0.2823 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 10:36:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.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, 03 Apr 2021 10:36:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:36:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:36:43: 1000000 INFO @ Sat, 03 Apr 2021 10:36:50: 2000000 INFO @ Sat, 03 Apr 2021 10:36:57: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 10:37:05: 4000000 INFO @ Sat, 03 Apr 2021 10:37:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.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, 03 Apr 2021 10:37:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:37:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:37:15: 5000000 INFO @ Sat, 03 Apr 2021 10:37:16: 1000000 INFO @ Sat, 03 Apr 2021 10:37:23: 6000000 INFO @ Sat, 03 Apr 2021 10:37:24: 2000000 INFO @ Sat, 03 Apr 2021 10:37:30: 7000000 INFO @ Sat, 03 Apr 2021 10:37:31: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 10:37:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.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, 03 Apr 2021 10:37:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 10:37:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 10:37:38: 8000000 INFO @ Sat, 03 Apr 2021 10:37:39: 4000000 INFO @ Sat, 03 Apr 2021 10:37:44: 1000000 INFO @ Sat, 03 Apr 2021 10:37:46: 9000000 INFO @ Sat, 03 Apr 2021 10:37:47: 5000000 INFO @ Sat, 03 Apr 2021 10:37:52: 2000000 INFO @ Sat, 03 Apr 2021 10:37:54: 10000000 INFO @ Sat, 03 Apr 2021 10:37:55: 6000000 INFO @ Sat, 03 Apr 2021 10:37:59: 3000000 INFO @ Sat, 03 Apr 2021 10:38:02: 11000000 INFO @ Sat, 03 Apr 2021 10:38:03: 7000000 INFO @ Sat, 03 Apr 2021 10:38:06: 4000000 INFO @ Sat, 03 Apr 2021 10:38:11: 12000000 INFO @ Sat, 03 Apr 2021 10:38:11: 8000000 INFO @ Sat, 03 Apr 2021 10:38:14: 5000000 INFO @ Sat, 03 Apr 2021 10:38:20: 9000000 INFO @ Sat, 03 Apr 2021 10:38:20: 13000000 INFO @ Sat, 03 Apr 2021 10:38:23: 6000000 INFO @ Sat, 03 Apr 2021 10:38:29: 10000000 INFO @ Sat, 03 Apr 2021 10:38:30: 14000000 INFO @ Sat, 03 Apr 2021 10:38:31: 7000000 INFO @ Sat, 03 Apr 2021 10:38:39: 8000000 INFO @ Sat, 03 Apr 2021 10:38:40: 11000000 INFO @ Sat, 03 Apr 2021 10:38:40: 15000000 INFO @ Sat, 03 Apr 2021 10:38:47: 9000000 INFO @ Sat, 03 Apr 2021 10:38:50: 16000000 INFO @ Sat, 03 Apr 2021 10:38:50: 12000000 INFO @ Sat, 03 Apr 2021 10:38:54: 10000000 INFO @ Sat, 03 Apr 2021 10:38:58: 17000000 INFO @ Sat, 03 Apr 2021 10:38:59: 13000000 INFO @ Sat, 03 Apr 2021 10:39:02: 11000000 INFO @ Sat, 03 Apr 2021 10:39:07: 18000000 INFO @ Sat, 03 Apr 2021 10:39:08: 14000000 INFO @ Sat, 03 Apr 2021 10:39:10: 12000000 INFO @ Sat, 03 Apr 2021 10:39:16: 19000000 INFO @ Sat, 03 Apr 2021 10:39:17: 15000000 INFO @ Sat, 03 Apr 2021 10:39:18: 13000000 INFO @ Sat, 03 Apr 2021 10:39:25: 20000000 INFO @ Sat, 03 Apr 2021 10:39:26: 14000000 INFO @ Sat, 03 Apr 2021 10:39:26: 16000000 INFO @ Sat, 03 Apr 2021 10:39:34: 15000000 INFO @ Sat, 03 Apr 2021 10:39:35: 21000000 INFO @ Sat, 03 Apr 2021 10:39:36: 17000000 INFO @ Sat, 03 Apr 2021 10:39:42: 16000000 INFO @ Sat, 03 Apr 2021 10:39:44: 22000000 INFO @ Sat, 03 Apr 2021 10:39:45: 18000000 INFO @ Sat, 03 Apr 2021 10:39:51: 17000000 INFO @ Sat, 03 Apr 2021 10:39:52: 23000000 INFO @ Sat, 03 Apr 2021 10:39:54: 19000000 INFO @ Sat, 03 Apr 2021 10:40:01: 24000000 INFO @ Sat, 03 Apr 2021 10:40:02: 18000000 INFO @ Sat, 03 Apr 2021 10:40:03: 20000000 INFO @ Sat, 03 Apr 2021 10:40:09: 25000000 INFO @ Sat, 03 Apr 2021 10:40:10: 19000000 INFO @ Sat, 03 Apr 2021 10:40:11: 21000000 INFO @ Sat, 03 Apr 2021 10:40:20: 26000000 INFO @ Sat, 03 Apr 2021 10:40:20: 20000000 INFO @ Sat, 03 Apr 2021 10:40:21: 22000000 INFO @ Sat, 03 Apr 2021 10:40:30: 21000000 INFO @ Sat, 03 Apr 2021 10:40:30: 27000000 INFO @ Sat, 03 Apr 2021 10:40:32: 23000000 INFO @ Sat, 03 Apr 2021 10:40:39: 28000000 INFO @ Sat, 03 Apr 2021 10:40:40: 22000000 INFO @ Sat, 03 Apr 2021 10:40:40: 24000000 INFO @ Sat, 03 Apr 2021 10:40:49: 29000000 INFO @ Sat, 03 Apr 2021 10:40:50: 25000000 INFO @ Sat, 03 Apr 2021 10:40:50: 23000000 INFO @ Sat, 03 Apr 2021 10:40:58: 30000000 INFO @ Sat, 03 Apr 2021 10:41:00: 26000000 INFO @ Sat, 03 Apr 2021 10:41:03: 24000000 INFO @ Sat, 03 Apr 2021 10:41:08: 31000000 INFO @ Sat, 03 Apr 2021 10:41:09: 27000000 INFO @ Sat, 03 Apr 2021 10:41:15: 25000000 INFO @ Sat, 03 Apr 2021 10:41:18: 32000000 INFO @ Sat, 03 Apr 2021 10:41:19: 28000000 INFO @ Sat, 03 Apr 2021 10:41:29: 26000000 INFO @ Sat, 03 Apr 2021 10:41:30: 33000000 INFO @ Sat, 03 Apr 2021 10:41:31: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 10:41:31: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 10:41:31: #1 total tags in treatment: 11641875 INFO @ Sat, 03 Apr 2021 10:41:31: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:41:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 10:41:32: #1 tags after filtering in treatment: 8979727 INFO @ Sat, 03 Apr 2021 10:41:32: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 10:41:32: #1 finished! INFO @ Sat, 03 Apr 2021 10:41:32: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:41:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:41:33: 29000000 INFO @ Sat, 03 Apr 2021 10:41:33: #2 number of paired peaks: 705 WARNING @ Sat, 03 Apr 2021 10:41:33: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Sat, 03 Apr 2021 10:41:33: start model_add_line... INFO @ Sat, 03 Apr 2021 10:41:33: start X-correlation... INFO @ Sat, 03 Apr 2021 10:41:33: end of X-cor INFO @ Sat, 03 Apr 2021 10:41:33: #2 finished! INFO @ Sat, 03 Apr 2021 10:41:33: #2 predicted fragment length is 133 bps INFO @ Sat, 03 Apr 2021 10:41:33: #2 alternative fragment length(s) may be 133,142 bps INFO @ Sat, 03 Apr 2021 10:41:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.05_model.r WARNING @ Sat, 03 Apr 2021 10:41:33: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:41:33: #2 You may need to consider one of the other alternative d(s): 133,142 WARNING @ Sat, 03 Apr 2021 10:41:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 10:41:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:41:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:41:43: 27000000 INFO @ Sat, 03 Apr 2021 10:41:45: 30000000 INFO @ Sat, 03 Apr 2021 10:41:56: 31000000 INFO @ Sat, 03 Apr 2021 10:42:00: 28000000 INFO @ Sat, 03 Apr 2021 10:42:00: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 10:42:08: 32000000 INFO @ Sat, 03 Apr 2021 10:42:15: 29000000 INFO @ Sat, 03 Apr 2021 10:42:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.05_peaks.xls INFO @ Sat, 03 Apr 2021 10:42:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:42:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.05_summits.bed INFO @ Sat, 03 Apr 2021 10:42:17: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10200 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 10:42:20: 33000000 INFO @ Sat, 03 Apr 2021 10:42:21: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 10:42:21: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 10:42:21: #1 total tags in treatment: 11641875 INFO @ Sat, 03 Apr 2021 10:42:21: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:42:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 10:42:21: #1 tags after filtering in treatment: 8979727 INFO @ Sat, 03 Apr 2021 10:42:21: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 10:42:21: #1 finished! INFO @ Sat, 03 Apr 2021 10:42:21: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:42:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:42:22: #2 number of paired peaks: 705 WARNING @ Sat, 03 Apr 2021 10:42:22: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Sat, 03 Apr 2021 10:42:22: start model_add_line... INFO @ Sat, 03 Apr 2021 10:42:22: start X-correlation... INFO @ Sat, 03 Apr 2021 10:42:22: end of X-cor INFO @ Sat, 03 Apr 2021 10:42:22: #2 finished! INFO @ Sat, 03 Apr 2021 10:42:22: #2 predicted fragment length is 133 bps INFO @ Sat, 03 Apr 2021 10:42:22: #2 alternative fragment length(s) may be 133,142 bps INFO @ Sat, 03 Apr 2021 10:42:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.10_model.r WARNING @ Sat, 03 Apr 2021 10:42:22: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:42:22: #2 You may need to consider one of the other alternative d(s): 133,142 WARNING @ Sat, 03 Apr 2021 10:42:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 10:42:22: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:42:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:42:25: 30000000 INFO @ Sat, 03 Apr 2021 10:42:37: 31000000 INFO @ Sat, 03 Apr 2021 10:42:47: 32000000 INFO @ Sat, 03 Apr 2021 10:42:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 10:42:56: 33000000 INFO @ Sat, 03 Apr 2021 10:42:57: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 10:42:57: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 10:42:57: #1 total tags in treatment: 11641875 INFO @ Sat, 03 Apr 2021 10:42:57: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 10:42:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 10:42:57: #1 tags after filtering in treatment: 8979727 INFO @ Sat, 03 Apr 2021 10:42:57: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 10:42:57: #1 finished! INFO @ Sat, 03 Apr 2021 10:42:57: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 10:42:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 10:42:58: #2 number of paired peaks: 705 WARNING @ Sat, 03 Apr 2021 10:42:58: Fewer paired peaks (705) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 705 pairs to build model! INFO @ Sat, 03 Apr 2021 10:42:58: start model_add_line... INFO @ Sat, 03 Apr 2021 10:42:58: start X-correlation... INFO @ Sat, 03 Apr 2021 10:42:58: end of X-cor INFO @ Sat, 03 Apr 2021 10:42:58: #2 finished! INFO @ Sat, 03 Apr 2021 10:42:58: #2 predicted fragment length is 133 bps INFO @ Sat, 03 Apr 2021 10:42:58: #2 alternative fragment length(s) may be 133,142 bps INFO @ Sat, 03 Apr 2021 10:42:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.20_model.r WARNING @ Sat, 03 Apr 2021 10:42:58: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 10:42:58: #2 You may need to consider one of the other alternative d(s): 133,142 WARNING @ Sat, 03 Apr 2021 10:42:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 10:42:58: #3 Call peaks... INFO @ Sat, 03 Apr 2021 10:42:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 10:43:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.10_peaks.xls INFO @ Sat, 03 Apr 2021 10:43:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:43:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.10_summits.bed INFO @ Sat, 03 Apr 2021 10:43:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4971 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 10:43:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 10:43:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.20_peaks.xls INFO @ Sat, 03 Apr 2021 10:43:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 10:43:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806723/SRX7806723.20_summits.bed INFO @ Sat, 03 Apr 2021 10:43:29: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1147 records, 4 fields): 4 millis CompletedMACS2peakCalling