Job ID = 5720165 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T12:49:56 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T12:53:19 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T13:02:10 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T13:02:50 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 32,260,840 reads read : 64,521,680 reads written : 64,521,680 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:03:09 32260840 reads; of these: 32260840 (100.00%) were paired; of these: 19673125 (60.98%) aligned concordantly 0 times 9131550 (28.31%) aligned concordantly exactly 1 time 3456165 (10.71%) aligned concordantly >1 times ---- 19673125 pairs aligned concordantly 0 times; of these: 7140849 (36.30%) aligned discordantly 1 time ---- 12532276 pairs aligned 0 times concordantly or discordantly; of these: 25064552 mates make up the pairs; of these: 21286802 (84.93%) aligned 0 times 1085246 (4.33%) aligned exactly 1 time 2692504 (10.74%) aligned >1 times 67.01% overall alignment rate Time searching: 01:03:10 Overall time: 01:03:10 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 32 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] 3343249 / 19401753 = 0.1723 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 15 Apr 2020 23:40:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.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 @ Wed, 15 Apr 2020 23:40:49: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:40:49: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:40:56: 1000000 INFO @ Wed, 15 Apr 2020 23:41:03: 2000000 INFO @ Wed, 15 Apr 2020 23:41:10: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 15 Apr 2020 23:41:17: 4000000 INFO @ Wed, 15 Apr 2020 23:41:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.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 @ Wed, 15 Apr 2020 23:41:18: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:41:18: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:41:23: 5000000 INFO @ Wed, 15 Apr 2020 23:41:25: 1000000 INFO @ Wed, 15 Apr 2020 23:41:30: 6000000 INFO @ Wed, 15 Apr 2020 23:41:33: 2000000 INFO @ Wed, 15 Apr 2020 23:41:37: 7000000 INFO @ Wed, 15 Apr 2020 23:41:39: 3000000 INFO @ Wed, 15 Apr 2020 23:41:44: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 15 Apr 2020 23:41:46: 4000000 INFO @ Wed, 15 Apr 2020 23:41:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.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 @ Wed, 15 Apr 2020 23:41:48: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:41:48: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:41:51: 9000000 INFO @ Wed, 15 Apr 2020 23:41:54: 5000000 INFO @ Wed, 15 Apr 2020 23:41:55: 1000000 INFO @ Wed, 15 Apr 2020 23:41:57: 10000000 INFO @ Wed, 15 Apr 2020 23:42:01: 6000000 INFO @ Wed, 15 Apr 2020 23:42:03: 2000000 INFO @ Wed, 15 Apr 2020 23:42:04: 11000000 INFO @ Wed, 15 Apr 2020 23:42:07: 7000000 INFO @ Wed, 15 Apr 2020 23:42:10: 3000000 INFO @ Wed, 15 Apr 2020 23:42:11: 12000000 INFO @ Wed, 15 Apr 2020 23:42:14: 8000000 INFO @ Wed, 15 Apr 2020 23:42:17: 4000000 INFO @ Wed, 15 Apr 2020 23:42:18: 13000000 INFO @ Wed, 15 Apr 2020 23:42:21: 9000000 INFO @ Wed, 15 Apr 2020 23:42:24: 5000000 INFO @ Wed, 15 Apr 2020 23:42:25: 14000000 INFO @ Wed, 15 Apr 2020 23:42:28: 10000000 INFO @ Wed, 15 Apr 2020 23:42:31: 6000000 INFO @ Wed, 15 Apr 2020 23:42:32: 15000000 INFO @ Wed, 15 Apr 2020 23:42:35: 11000000 INFO @ Wed, 15 Apr 2020 23:42:38: 7000000 INFO @ Wed, 15 Apr 2020 23:42:39: 16000000 INFO @ Wed, 15 Apr 2020 23:42:42: 12000000 INFO @ Wed, 15 Apr 2020 23:42:44: 8000000 INFO @ Wed, 15 Apr 2020 23:42:46: 17000000 INFO @ Wed, 15 Apr 2020 23:42:50: 13000000 INFO @ Wed, 15 Apr 2020 23:42:51: 9000000 INFO @ Wed, 15 Apr 2020 23:42:53: 18000000 INFO @ Wed, 15 Apr 2020 23:42:56: 14000000 INFO @ Wed, 15 Apr 2020 23:42:58: 10000000 INFO @ Wed, 15 Apr 2020 23:43:00: 19000000 INFO @ Wed, 15 Apr 2020 23:43:03: 15000000 INFO @ Wed, 15 Apr 2020 23:43:05: 11000000 INFO @ Wed, 15 Apr 2020 23:43:08: 20000000 INFO @ Wed, 15 Apr 2020 23:43:11: 16000000 INFO @ Wed, 15 Apr 2020 23:43:12: 12000000 INFO @ Wed, 15 Apr 2020 23:43:15: 21000000 INFO @ Wed, 15 Apr 2020 23:43:18: 17000000 INFO @ Wed, 15 Apr 2020 23:43:19: 13000000 INFO @ Wed, 15 Apr 2020 23:43:22: 22000000 INFO @ Wed, 15 Apr 2020 23:43:25: 18000000 INFO @ Wed, 15 Apr 2020 23:43:26: 14000000 INFO @ Wed, 15 Apr 2020 23:43:29: 23000000 INFO @ Wed, 15 Apr 2020 23:43:32: 19000000 INFO @ Wed, 15 Apr 2020 23:43:33: 15000000 INFO @ Wed, 15 Apr 2020 23:43:36: 24000000 INFO @ Wed, 15 Apr 2020 23:43:39: 20000000 INFO @ Wed, 15 Apr 2020 23:43:40: 16000000 INFO @ Wed, 15 Apr 2020 23:43:43: 25000000 INFO @ Wed, 15 Apr 2020 23:43:46: 21000000 INFO @ Wed, 15 Apr 2020 23:43:48: 17000000 INFO @ Wed, 15 Apr 2020 23:43:50: 26000000 INFO @ Wed, 15 Apr 2020 23:43:53: 22000000 INFO @ Wed, 15 Apr 2020 23:43:55: 18000000 INFO @ Wed, 15 Apr 2020 23:43:57: 27000000 INFO @ Wed, 15 Apr 2020 23:44:01: 23000000 INFO @ Wed, 15 Apr 2020 23:44:02: 19000000 INFO @ Wed, 15 Apr 2020 23:44:04: 28000000 INFO @ Wed, 15 Apr 2020 23:44:09: 24000000 INFO @ Wed, 15 Apr 2020 23:44:10: 20000000 INFO @ Wed, 15 Apr 2020 23:44:11: 29000000 INFO @ Wed, 15 Apr 2020 23:44:16: 25000000 INFO @ Wed, 15 Apr 2020 23:44:18: 21000000 INFO @ Wed, 15 Apr 2020 23:44:18: 30000000 INFO @ Wed, 15 Apr 2020 23:44:23: 26000000 INFO @ Wed, 15 Apr 2020 23:44:25: 22000000 INFO @ Wed, 15 Apr 2020 23:44:26: 31000000 INFO @ Wed, 15 Apr 2020 23:44:30: 27000000 INFO @ Wed, 15 Apr 2020 23:44:32: 23000000 INFO @ Wed, 15 Apr 2020 23:44:33: 32000000 INFO @ Wed, 15 Apr 2020 23:44:37: 28000000 INFO @ Wed, 15 Apr 2020 23:44:39: 24000000 INFO @ Wed, 15 Apr 2020 23:44:40: 33000000 INFO @ Wed, 15 Apr 2020 23:44:44: 29000000 INFO @ Wed, 15 Apr 2020 23:44:46: 25000000 INFO @ Wed, 15 Apr 2020 23:44:47: 34000000 INFO @ Wed, 15 Apr 2020 23:44:51: 30000000 INFO @ Wed, 15 Apr 2020 23:44:53: 26000000 INFO @ Wed, 15 Apr 2020 23:44:54: 35000000 INFO @ Wed, 15 Apr 2020 23:44:58: 31000000 INFO @ Wed, 15 Apr 2020 23:45:00: 27000000 INFO @ Wed, 15 Apr 2020 23:45:00: 36000000 INFO @ Wed, 15 Apr 2020 23:45:04: #1 tag size is determined as 150 bps INFO @ Wed, 15 Apr 2020 23:45:04: #1 tag size = 150 INFO @ Wed, 15 Apr 2020 23:45:04: #1 total tags in treatment: 10176938 INFO @ Wed, 15 Apr 2020 23:45:04: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:45:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:45:04: #1 tags after filtering in treatment: 7984771 INFO @ Wed, 15 Apr 2020 23:45:04: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 15 Apr 2020 23:45:04: #1 finished! INFO @ Wed, 15 Apr 2020 23:45:04: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:45:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:45:05: #2 number of paired peaks: 570 WARNING @ Wed, 15 Apr 2020 23:45:05: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Wed, 15 Apr 2020 23:45:05: start model_add_line... INFO @ Wed, 15 Apr 2020 23:45:05: start X-correlation... INFO @ Wed, 15 Apr 2020 23:45:05: end of X-cor INFO @ Wed, 15 Apr 2020 23:45:05: #2 finished! INFO @ Wed, 15 Apr 2020 23:45:05: #2 predicted fragment length is 221 bps INFO @ Wed, 15 Apr 2020 23:45:05: #2 alternative fragment length(s) may be 221 bps INFO @ Wed, 15 Apr 2020 23:45:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.05_model.r WARNING @ Wed, 15 Apr 2020 23:45:05: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:45:05: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Wed, 15 Apr 2020 23:45:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:45:05: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:45:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:45:06: 32000000 INFO @ Wed, 15 Apr 2020 23:45:07: 28000000 INFO @ Wed, 15 Apr 2020 23:45:13: 33000000 INFO @ Wed, 15 Apr 2020 23:45:14: 29000000 INFO @ Wed, 15 Apr 2020 23:45:20: 34000000 INFO @ Wed, 15 Apr 2020 23:45:21: 30000000 INFO @ Wed, 15 Apr 2020 23:45:26: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:45:26: 35000000 INFO @ Wed, 15 Apr 2020 23:45:28: 31000000 INFO @ Wed, 15 Apr 2020 23:45:33: 36000000 INFO @ Wed, 15 Apr 2020 23:45:35: 32000000 INFO @ Wed, 15 Apr 2020 23:45:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:45:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:45:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.05_summits.bed INFO @ Wed, 15 Apr 2020 23:45:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (807 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:45:37: #1 tag size is determined as 150 bps INFO @ Wed, 15 Apr 2020 23:45:37: #1 tag size = 150 INFO @ Wed, 15 Apr 2020 23:45:37: #1 total tags in treatment: 10176938 INFO @ Wed, 15 Apr 2020 23:45:37: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:45:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:45:37: #1 tags after filtering in treatment: 7984771 INFO @ Wed, 15 Apr 2020 23:45:37: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 15 Apr 2020 23:45:37: #1 finished! INFO @ Wed, 15 Apr 2020 23:45:37: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:45:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:45:37: #2 number of paired peaks: 570 WARNING @ Wed, 15 Apr 2020 23:45:37: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Wed, 15 Apr 2020 23:45:37: start model_add_line... INFO @ Wed, 15 Apr 2020 23:45:38: start X-correlation... INFO @ Wed, 15 Apr 2020 23:45:38: end of X-cor INFO @ Wed, 15 Apr 2020 23:45:38: #2 finished! INFO @ Wed, 15 Apr 2020 23:45:38: #2 predicted fragment length is 221 bps INFO @ Wed, 15 Apr 2020 23:45:38: #2 alternative fragment length(s) may be 221 bps INFO @ Wed, 15 Apr 2020 23:45:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.10_model.r WARNING @ Wed, 15 Apr 2020 23:45:38: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:45:38: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Wed, 15 Apr 2020 23:45:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:45:38: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:45:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:45:42: 33000000 INFO @ Wed, 15 Apr 2020 23:45:49: 34000000 INFO @ Wed, 15 Apr 2020 23:45:56: 35000000 INFO @ Wed, 15 Apr 2020 23:45:59: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:46:02: 36000000 INFO @ Wed, 15 Apr 2020 23:46:06: #1 tag size is determined as 150 bps INFO @ Wed, 15 Apr 2020 23:46:06: #1 tag size = 150 INFO @ Wed, 15 Apr 2020 23:46:06: #1 total tags in treatment: 10176938 INFO @ Wed, 15 Apr 2020 23:46:06: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:46:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:46:06: #1 tags after filtering in treatment: 7984771 INFO @ Wed, 15 Apr 2020 23:46:06: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 15 Apr 2020 23:46:06: #1 finished! INFO @ Wed, 15 Apr 2020 23:46:06: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:46:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:46:07: #2 number of paired peaks: 570 WARNING @ Wed, 15 Apr 2020 23:46:07: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Wed, 15 Apr 2020 23:46:07: start model_add_line... INFO @ Wed, 15 Apr 2020 23:46:07: start X-correlation... INFO @ Wed, 15 Apr 2020 23:46:07: end of X-cor INFO @ Wed, 15 Apr 2020 23:46:07: #2 finished! INFO @ Wed, 15 Apr 2020 23:46:07: #2 predicted fragment length is 221 bps INFO @ Wed, 15 Apr 2020 23:46:07: #2 alternative fragment length(s) may be 221 bps INFO @ Wed, 15 Apr 2020 23:46:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.20_model.r WARNING @ Wed, 15 Apr 2020 23:46:07: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:46:07: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Wed, 15 Apr 2020 23:46:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:46:07: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:46:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:46:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:46:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:46:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.10_summits.bed INFO @ Wed, 15 Apr 2020 23:46:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (381 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:46:28: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:46:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:46:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:46:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619536/SRX6619536.20_summits.bed INFO @ Wed, 15 Apr 2020 23:46:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (197 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。