Job ID = 12264742 SRX = SRX2332995 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26099622 spots for SRR5000675/SRR5000675.sra Written 26099622 spots for SRR5000675/SRR5000675.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265454 ("srTce11") 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: 00:37:06 26099622 reads; of these: 26099622 (100.00%) were paired; of these: 12933407 (49.55%) aligned concordantly 0 times 10604474 (40.63%) aligned concordantly exactly 1 time 2561741 (9.82%) aligned concordantly >1 times ---- 12933407 pairs aligned concordantly 0 times; of these: 4513718 (34.90%) aligned discordantly 1 time ---- 8419689 pairs aligned 0 times concordantly or discordantly; of these: 16839378 mates make up the pairs; of these: 14575367 (86.56%) aligned 0 times 834737 (4.96%) aligned exactly 1 time 1429274 (8.49%) aligned >1 times 72.08% overall alignment rate Time searching: 00:37:06 Overall time: 00:37:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 3373171 / 17587171 = 0.1918 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 06:56:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.bam'] # control file = None # effective genome size = 9.00e+07 # 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 06:56:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:56:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:56:20: 1000000 INFO @ Sat, 03 Apr 2021 06:56:26: 2000000 INFO @ Sat, 03 Apr 2021 06:56:33: 3000000 INFO @ Sat, 03 Apr 2021 06:56:40: 4000000 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 06:56:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.bam'] # control file = None # effective genome size = 9.00e+07 # 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 06:56:43: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:56:43: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:56:47: 5000000 INFO @ Sat, 03 Apr 2021 06:56:51: 1000000 INFO @ Sat, 03 Apr 2021 06:56:54: 6000000 INFO @ Sat, 03 Apr 2021 06:56:59: 2000000 INFO @ Sat, 03 Apr 2021 06:57:02: 7000000 INFO @ Sat, 03 Apr 2021 06:57:07: 3000000 INFO @ Sat, 03 Apr 2021 06:57:09: 8000000 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 06:57:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.bam'] # control file = None # effective genome size = 9.00e+07 # 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 06:57:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:57:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:57:15: 4000000 INFO @ Sat, 03 Apr 2021 06:57:16: 9000000 INFO @ Sat, 03 Apr 2021 06:57:21: 1000000 INFO @ Sat, 03 Apr 2021 06:57:23: 5000000 INFO @ Sat, 03 Apr 2021 06:57:23: 10000000 INFO @ Sat, 03 Apr 2021 06:57:30: 2000000 INFO @ Sat, 03 Apr 2021 06:57:30: 11000000 INFO @ Sat, 03 Apr 2021 06:57:31: 6000000 INFO @ Sat, 03 Apr 2021 06:57:38: 12000000 INFO @ Sat, 03 Apr 2021 06:57:38: 3000000 INFO @ Sat, 03 Apr 2021 06:57:39: 7000000 INFO @ Sat, 03 Apr 2021 06:57:45: 13000000 INFO @ Sat, 03 Apr 2021 06:57:46: 4000000 INFO @ Sat, 03 Apr 2021 06:57:47: 8000000 INFO @ Sat, 03 Apr 2021 06:57:52: 14000000 INFO @ Sat, 03 Apr 2021 06:57:54: 5000000 INFO @ Sat, 03 Apr 2021 06:57:55: 9000000 INFO @ Sat, 03 Apr 2021 06:58:00: 15000000 INFO @ Sat, 03 Apr 2021 06:58:02: 10000000 INFO @ Sat, 03 Apr 2021 06:58:03: 6000000 INFO @ Sat, 03 Apr 2021 06:58:07: 16000000 INFO @ Sat, 03 Apr 2021 06:58:10: 11000000 INFO @ Sat, 03 Apr 2021 06:58:11: 7000000 INFO @ Sat, 03 Apr 2021 06:58:14: 17000000 INFO @ Sat, 03 Apr 2021 06:58:18: 12000000 INFO @ Sat, 03 Apr 2021 06:58:19: 8000000 INFO @ Sat, 03 Apr 2021 06:58:22: 18000000 INFO @ Sat, 03 Apr 2021 06:58:26: 13000000 INFO @ Sat, 03 Apr 2021 06:58:27: 9000000 INFO @ Sat, 03 Apr 2021 06:58:29: 19000000 INFO @ Sat, 03 Apr 2021 06:58:34: 14000000 INFO @ Sat, 03 Apr 2021 06:58:35: 10000000 INFO @ Sat, 03 Apr 2021 06:58:37: 20000000 INFO @ Sat, 03 Apr 2021 06:58:42: 15000000 INFO @ Sat, 03 Apr 2021 06:58:43: 11000000 INFO @ Sat, 03 Apr 2021 06:58:44: 21000000 INFO @ Sat, 03 Apr 2021 06:58:50: 16000000 INFO @ Sat, 03 Apr 2021 06:58:51: 12000000 INFO @ Sat, 03 Apr 2021 06:58:52: 22000000 INFO @ Sat, 03 Apr 2021 06:58:58: 17000000 INFO @ Sat, 03 Apr 2021 06:58:58: 13000000 INFO @ Sat, 03 Apr 2021 06:58:59: 23000000 INFO @ Sat, 03 Apr 2021 06:59:06: 18000000 INFO @ Sat, 03 Apr 2021 06:59:06: 24000000 INFO @ Sat, 03 Apr 2021 06:59:06: 14000000 INFO @ Sat, 03 Apr 2021 06:59:13: 25000000 INFO @ Sat, 03 Apr 2021 06:59:14: 19000000 INFO @ Sat, 03 Apr 2021 06:59:14: 15000000 INFO @ Sat, 03 Apr 2021 06:59:20: 26000000 INFO @ Sat, 03 Apr 2021 06:59:22: 20000000 INFO @ Sat, 03 Apr 2021 06:59:23: 16000000 INFO @ Sat, 03 Apr 2021 06:59:27: 27000000 INFO @ Sat, 03 Apr 2021 06:59:30: 21000000 INFO @ Sat, 03 Apr 2021 06:59:31: 17000000 INFO @ Sat, 03 Apr 2021 06:59:34: 28000000 INFO @ Sat, 03 Apr 2021 06:59:38: 22000000 INFO @ Sat, 03 Apr 2021 06:59:39: 18000000 INFO @ Sat, 03 Apr 2021 06:59:41: 29000000 INFO @ Sat, 03 Apr 2021 06:59:46: 23000000 INFO @ Sat, 03 Apr 2021 06:59:47: 19000000 INFO @ Sat, 03 Apr 2021 06:59:48: 30000000 INFO @ Sat, 03 Apr 2021 06:59:54: 24000000 INFO @ Sat, 03 Apr 2021 06:59:54: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:59:54: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:59:54: #1 total tags in treatment: 10303031 INFO @ Sat, 03 Apr 2021 06:59:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:59:54: #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 06:59:55: #1 tags after filtering in treatment: 7000349 INFO @ Sat, 03 Apr 2021 06:59:55: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 06:59:55: #1 finished! INFO @ Sat, 03 Apr 2021 06:59:55: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:59:55: 20000000 INFO @ Sat, 03 Apr 2021 06:59:55: #2 number of paired peaks: 297 WARNING @ Sat, 03 Apr 2021 06:59:55: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Sat, 03 Apr 2021 06:59:55: start model_add_line... INFO @ Sat, 03 Apr 2021 06:59:55: start X-correlation... INFO @ Sat, 03 Apr 2021 06:59:55: end of X-cor INFO @ Sat, 03 Apr 2021 06:59:55: #2 finished! INFO @ Sat, 03 Apr 2021 06:59:55: #2 predicted fragment length is 154 bps INFO @ Sat, 03 Apr 2021 06:59:55: #2 alternative fragment length(s) may be 4,149,154 bps INFO @ Sat, 03 Apr 2021 06:59:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.05_model.r WARNING @ Sat, 03 Apr 2021 06:59:55: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:59:55: #2 You may need to consider one of the other alternative d(s): 4,149,154 WARNING @ Sat, 03 Apr 2021 06:59:55: #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 06:59:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:59:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:00:02: 25000000 INFO @ Sat, 03 Apr 2021 07:00:03: 21000000 INFO @ Sat, 03 Apr 2021 07:00:09: 26000000 INFO @ Sat, 03 Apr 2021 07:00:11: 22000000 INFO @ Sat, 03 Apr 2021 07:00:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:00:17: 27000000 INFO @ Sat, 03 Apr 2021 07:00:19: 23000000 INFO @ Sat, 03 Apr 2021 07:00:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:00:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:00:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.05_summits.bed INFO @ Sat, 03 Apr 2021 07:00:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1897 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:00:25: 28000000 INFO @ Sat, 03 Apr 2021 07:00:26: 24000000 INFO @ Sat, 03 Apr 2021 07:00:32: 29000000 INFO @ Sat, 03 Apr 2021 07:00:34: 25000000 INFO @ Sat, 03 Apr 2021 07:00:40: 30000000 INFO @ Sat, 03 Apr 2021 07:00:42: 26000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:00:46: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:00:46: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:00:46: #1 total tags in treatment: 10303031 INFO @ Sat, 03 Apr 2021 07:00:46: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:00:46: #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 07:00:47: #1 tags after filtering in treatment: 7000349 INFO @ Sat, 03 Apr 2021 07:00:47: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 07:00:47: #1 finished! INFO @ Sat, 03 Apr 2021 07:00:47: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:00:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:00:47: #2 number of paired peaks: 297 WARNING @ Sat, 03 Apr 2021 07:00:47: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Sat, 03 Apr 2021 07:00:47: start model_add_line... INFO @ Sat, 03 Apr 2021 07:00:47: start X-correlation... INFO @ Sat, 03 Apr 2021 07:00:47: end of X-cor INFO @ Sat, 03 Apr 2021 07:00:47: #2 finished! INFO @ Sat, 03 Apr 2021 07:00:47: #2 predicted fragment length is 154 bps INFO @ Sat, 03 Apr 2021 07:00:47: #2 alternative fragment length(s) may be 4,149,154 bps INFO @ Sat, 03 Apr 2021 07:00:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.10_model.r WARNING @ Sat, 03 Apr 2021 07:00:47: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:00:47: #2 You may need to consider one of the other alternative d(s): 4,149,154 WARNING @ Sat, 03 Apr 2021 07:00:47: #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 07:00:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:00:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:00:50: 27000000 INFO @ Sat, 03 Apr 2021 07:00:57: 28000000 INFO @ Sat, 03 Apr 2021 07:01:05: 29000000 INFO @ Sat, 03 Apr 2021 07:01:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:01:12: 30000000 INFO @ Sat, 03 Apr 2021 07:01:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:01:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:01:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.10_summits.bed INFO @ Sat, 03 Apr 2021 07:01:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (695 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:01:19: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 07:01:19: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 07:01:19: #1 total tags in treatment: 10303031 INFO @ Sat, 03 Apr 2021 07:01:19: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:01:19: #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 07:01:19: #1 tags after filtering in treatment: 7000349 INFO @ Sat, 03 Apr 2021 07:01:19: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 07:01:19: #1 finished! INFO @ Sat, 03 Apr 2021 07:01:19: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:01:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:01:20: #2 number of paired peaks: 297 WARNING @ Sat, 03 Apr 2021 07:01:20: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Sat, 03 Apr 2021 07:01:20: start model_add_line... INFO @ Sat, 03 Apr 2021 07:01:20: start X-correlation... INFO @ Sat, 03 Apr 2021 07:01:20: end of X-cor INFO @ Sat, 03 Apr 2021 07:01:20: #2 finished! INFO @ Sat, 03 Apr 2021 07:01:20: #2 predicted fragment length is 154 bps INFO @ Sat, 03 Apr 2021 07:01:20: #2 alternative fragment length(s) may be 4,149,154 bps INFO @ Sat, 03 Apr 2021 07:01:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.20_model.r WARNING @ Sat, 03 Apr 2021 07:01:20: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:01:20: #2 You may need to consider one of the other alternative d(s): 4,149,154 WARNING @ Sat, 03 Apr 2021 07:01:20: #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 07:01:20: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:01:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:01:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:01:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:01:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:01:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2332995/SRX2332995.20_summits.bed INFO @ Sat, 03 Apr 2021 07:01:47: Done! pass1 - making usageList (6 chroms): 6 millis pass2 - checking and writing primary data (178 records, 4 fields): 3 millis CompletedMACS2peakCalling