I tried running full analysis on TransPi with the following command:
"./nextflow -bg run TransPi.nf --all --reads '/home/geninfo/cassianoriyu/RNA_Millepora/AC_422/AC422_S687_S14_L001_R[1,2].fastq.gz' \ --k 25,35,55,75,85 --maxReadLen 100 --outdir Results_AC422 -profile conda --myConda"
But I get an error message at the very beginning:
"Error executing process > 'fastp (AC422_S687_S14_L001_R)'
Caused by:
Process fastp (AC422_S687_S14_L001_R) terminated with an error exit status (1)
Command error:
-G, --disable_trim_poly_g disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data
-x, --trim_poly_x enable polyX trimming in 3' ends.
--poly_x_min_len the minimum length to detect polyX in the read tail. 10 by default. (int [=10])
-5, --cut_front move a sliding window from front (5') to tail, drop the bases in the window if its mean quality < threshold, stop otherwise.
-3, --cut_tail move a sliding window from tail (3') to front, drop the bases in the window if its mean quality < threshold, stop otherwise.
-r, --cut_right move a sliding window from front to tail, if meet one window with mean quality < threshold, drop the bases in the window and the right part, and then stop.
-W, --cut_window_size the window size option shared by cut_front, cut_tail or cut_sliding. Range: 1~1000, default: 4 (int [=4])
-M, --cut_mean_quality the mean quality requirement option shared by cut_front, cut_tail or cut_sliding. Range: 1~36 default: 20 (Q20) (int [=20])
--cut_front_window_size the window size option of cut_front, default to cut_window_size if not specified (int [=4])
--cut_front_mean_quality the mean quality requirement option for cut_front, default to cut_mean_quality if not specified (int [=20])
--cut_tail_window_size the window size option of cut_tail, default to cut_window_size if not specified (int [=4])
--cut_tail_mean_quality the mean quality requirement option for cut_tail, default to cut_mean_quality if not specified (int [=20])
--cut_right_window_size the window size option of cut_right, default to cut_window_size if not specified (int [=4])
--cut_right_mean_quality the mean quality requirement option for cut_right, default to cut_mean_quality if not specified (int [=20])
-Q, --disable_quality_filtering quality filtering is enabled by default. If this option is specified, quality filtering is disabled
-q, --qualified_quality_phred the quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified. (int [=15])
-u, --unqualified_percent_limit how many percents of bases are allowed to be unqualified (0~100). Default 40 means 40% (int [=40])
-n, --n_base_limit if one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5 (int [=5])
-e, --average_qual if one read's average quality score <avg_qual, then this read/pair is discarded. Default 0 means no requirement (int [=0])
-L, --disable_length_filtering length filtering is enabled by default. If this option is specified, length filtering is disabled
-l, --length_required reads shorter than length_required will be discarded, default is 15. (int [=15])
--length_limit reads longer than length_limit will be discarded, default 0 means no limitation. (int [=0])
-y, --low_complexity_filter enable low complexity filter. The complexity is defined as the percentage of base that is different from its next base (base[i] != base[i+1]).
-Y, --complexity_threshold the threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required. (int [=30])
--filter_by_index1 specify a file contains a list of barcodes of index1 to be filtered out, one barcode per line (string [=])
--filter_by_index2 specify a file contains a list of barcodes of index2 to be filtered out, one barcode per line (string [=])
--filter_by_index_threshold the allowed difference of index barcode for index filtering, default 0 means completely identical. (int [=0])
-c, --correction enable base correction in overlapped regions (only for PE data), default is disabled
--overlap_len_require the minimum length to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. 30 by default. (int [=30])
--overlap_diff_limit the maximum number of mismatched bases to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. 5 by default. (int [=5])
--overlap_diff_percent_limit the maximum percentage of mismatched bases to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. Default 20 means 20%. (int [=20])
-U, --umi enable unique molecular identifier (UMI) preprocessing
--umi_loc specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none (string [=])
--umi_len if the UMI is in read1/read2, its length should be provided (int [=0])
--umi_prefix if specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No prefix by default (string [=])
--umi_skip if the UMI is in read1/read2, fastp can skip several bases following UMI, default is 0 (int [=0])
-p, --overrepresentation_analysis enable overrepresented sequence analysis.
-P, --overrepresentation_sampling one in (--overrepresentation_sampling) reads will be computed for overrepresentation analysis (1~10000), smaller is slower, default is 20. (int [=20])
-j, --json the json format report file name (string [=fastp.json])
-h, --html the html format report file name (string [=fastp.html])
-R, --report_title should be quoted with ' or ", default is "fastp report" (string [=fastp report])
-w, --thread worker thread number, default is 3 (int [=3])
-s, --split split output by limiting total split file number with this option (2~999), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (int [=0])
-S, --split_by_lines split output by limiting lines of each file with this option(>=1000), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (long [=0])
-d, --split_prefix_digits the digits for the sequential number padding (1~10), default is 4, so the filename will be padded as 0001.xxx, 0 to disable padding (int [=4])
--cut_by_quality5 DEPRECATED, use --cut_front instead.
--cut_by_quality3 DEPRECATED, use --cut_tail instead.
--cut_by_quality_aggressive DEPRECATED, use --cut_right instead.
--discard_unmerged DEPRECATED, no effect now, see the introduction for merging.
-?, --help print this message"
I have no idea what's causing this error. I tried manually installing fastp, and fastp different versions. Also tried reinstalling TransPi but nothing changed.
Does anyone has any clue on how to solve this?
Hi,
I tried running full analysis on TransPi with the following command: "./nextflow -bg run TransPi.nf --all --reads '/home/geninfo/cassianoriyu/RNA_Millepora/AC_422/AC422_S687_S14_L001_R[1,2].fastq.gz' \ --k 25,35,55,75,85 --maxReadLen 100 --outdir Results_AC422 -profile conda --myConda"
But I get an error message at the very beginning: "Error executing process > 'fastp (AC422_S687_S14_L001_R)'
Caused by: Process fastp (AC422_S687_S14_L001_R) terminated with an error exit status (1)
Command executed: fastp -i AC422_S687_S14_L001_R1.fastq.gz -I AC422_S687_S14_L001_R2.fastq.gz -o left-AC422_S687_S14_L001_R.filter.fq -O right-AC422_S687_S14_L001_R.filter.fq --detect_adapter_for_pe --average_qual null --overrepresentation_analysis --html AC422_S687_S14_L001_R.fastp.html --json AC422_S687_S14_L001_R.fastp.json --thread 1 --report_title AC422_S687_S14_L001_R
v=$( fastp --version 2>&1 | awk '{print $2}' ) echo "fastp: $v" >fastp.version.txt
Command exit status: 1
Command output: (empty)
Command error: -G, --disable_trim_poly_g disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data -x, --trim_poly_x enable polyX trimming in 3' ends. --poly_x_min_len the minimum length to detect polyX in the read tail. 10 by default. (int [=10]) -5, --cut_front move a sliding window from front (5') to tail, drop the bases in the window if its mean quality < threshold, stop otherwise. -3, --cut_tail move a sliding window from tail (3') to front, drop the bases in the window if its mean quality < threshold, stop otherwise. -r, --cut_right move a sliding window from front to tail, if meet one window with mean quality < threshold, drop the bases in the window and the right part, and then stop. -W, --cut_window_size the window size option shared by cut_front, cut_tail or cut_sliding. Range: 1~1000, default: 4 (int [=4]) -M, --cut_mean_quality the mean quality requirement option shared by cut_front, cut_tail or cut_sliding. Range: 1~36 default: 20 (Q20) (int [=20]) --cut_front_window_size the window size option of cut_front, default to cut_window_size if not specified (int [=4]) --cut_front_mean_quality the mean quality requirement option for cut_front, default to cut_mean_quality if not specified (int [=20]) --cut_tail_window_size the window size option of cut_tail, default to cut_window_size if not specified (int [=4]) --cut_tail_mean_quality the mean quality requirement option for cut_tail, default to cut_mean_quality if not specified (int [=20]) --cut_right_window_size the window size option of cut_right, default to cut_window_size if not specified (int [=4]) --cut_right_mean_quality the mean quality requirement option for cut_right, default to cut_mean_quality if not specified (int [=20]) -Q, --disable_quality_filtering quality filtering is enabled by default. If this option is specified, quality filtering is disabled -q, --qualified_quality_phred the quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified. (int [=15]) -u, --unqualified_percent_limit how many percents of bases are allowed to be unqualified (0~100). Default 40 means 40% (int [=40]) -n, --n_base_limit if one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5 (int [=5]) -e, --average_qual if one read's average quality score <avg_qual, then this read/pair is discarded. Default 0 means no requirement (int [=0]) -L, --disable_length_filtering length filtering is enabled by default. If this option is specified, length filtering is disabled -l, --length_required reads shorter than length_required will be discarded, default is 15. (int [=15]) --length_limit reads longer than length_limit will be discarded, default 0 means no limitation. (int [=0]) -y, --low_complexity_filter enable low complexity filter. The complexity is defined as the percentage of base that is different from its next base (base[i] != base[i+1]). -Y, --complexity_threshold the threshold for low complexity filter (0~100). Default is 30, which means 30% complexity is required. (int [=30]) --filter_by_index1 specify a file contains a list of barcodes of index1 to be filtered out, one barcode per line (string [=]) --filter_by_index2 specify a file contains a list of barcodes of index2 to be filtered out, one barcode per line (string [=]) --filter_by_index_threshold the allowed difference of index barcode for index filtering, default 0 means completely identical. (int [=0]) -c, --correction enable base correction in overlapped regions (only for PE data), default is disabled --overlap_len_require the minimum length to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. 30 by default. (int [=30]) --overlap_diff_limit the maximum number of mismatched bases to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. 5 by default. (int [=5]) --overlap_diff_percent_limit the maximum percentage of mismatched bases to detect overlapped region of PE reads. This will affect overlap analysis based PE merge, adapter trimming and correction. Default 20 means 20%. (int [=20]) -U, --umi enable unique molecular identifier (UMI) preprocessing --umi_loc specify the location of UMI, can be (index1/index2/read1/read2/per_index/per_read, default is none (string [=]) --umi_len if the UMI is in read1/read2, its length should be provided (int [=0]) --umi_prefix if specified, an underline will be used to connect prefix and UMI (i.e. prefix=UMI, UMI=AATTCG, final=UMI_AATTCG). No prefix by default (string [=]) --umi_skip if the UMI is in read1/read2, fastp can skip several bases following UMI, default is 0 (int [=0]) -p, --overrepresentation_analysis enable overrepresented sequence analysis. -P, --overrepresentation_sampling one in (--overrepresentation_sampling) reads will be computed for overrepresentation analysis (1~10000), smaller is slower, default is 20. (int [=20]) -j, --json the json format report file name (string [=fastp.json]) -h, --html the html format report file name (string [=fastp.html]) -R, --report_title should be quoted with ' or ", default is "fastp report" (string [=fastp report]) -w, --thread worker thread number, default is 3 (int [=3]) -s, --split split output by limiting total split file number with this option (2~999), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (int [=0]) -S, --split_by_lines split output by limiting lines of each file with this option(>=1000), a sequential number prefix will be added to output name ( 0001.out.fq, 0002.out.fq...), disabled by default (long [=0]) -d, --split_prefix_digits the digits for the sequential number padding (1~10), default is 4, so the filename will be padded as 0001.xxx, 0 to disable padding (int [=4]) --cut_by_quality5 DEPRECATED, use --cut_front instead. --cut_by_quality3 DEPRECATED, use --cut_tail instead. --cut_by_quality_aggressive DEPRECATED, use --cut_right instead. --discard_unmerged DEPRECATED, no effect now, see the introduction for merging. -?, --help print this message"
I have no idea what's causing this error. I tried manually installing fastp, and fastp different versions. Also tried reinstalling TransPi but nothing changed. Does anyone has any clue on how to solve this?
Thanks.