carlyraea
commented
5 years ago Sorry- initial params file got cut off: data8 ## [0] [assembly_name]: Assembly name. Used to name output directories for assembly steps /scratch/summit/caan8813/data8 ## [1] [project_dir]: Project dir (made in curdir if not present)
[2] [raw_fastq_path]: Location of raw non-demultiplexed fastq files
## [3] [barcodes_path]: Location of barcodes file/scratch/summit/caan8813/cladonia_all_demuxed/*.fq ## [4] [sorted_fastq_path]: Location of demultiplexed/sorted fastq files denovo ## [5] [assembly_method]: Assembly method (denovo, reference, denovo+reference, denovo-reference)
isaacovercast
iPyrad is failing at Step 2
Step 2: Filtering reads Skipping Sample orig_cladonia_demux_Cladonia_sp2; Already filtered. Use force argument to overwrite.
Skipping Sample orig_cladonia_demux_Stereocaulon_rivulorum; Already filtered. Use force argument to overwrite.
Skipping Sample orig_cladonia_demux_Cladonia_cervicornis_verticillata; Already filtered. Use force argument to overwrite.
Skipping Sample orig_cladonia_demux_Cladonia_caroliniana2; Already filtered. Use force argument to overwrite.
Skipping Sample orig_cladonia_demux_Cladonia_caroliniana3; Already filtered. Use force argument to overwrite.
Skipping Sample carly_justin_demux_Cladonia_krempelhuberi_redo; Already filtered. Use force argument to overwrite. [.....]
Then it processes reads for a moment before giving this error:
found an error in step2; see ipyrad_log.txt found an error in step2; see ipyrad_log.txt found an error in step2; see ipyrad_log.txt found an error in step2; see ipyrad_log.txt found an error in step2; see ipyrad_log.txt found an error in step2; see ipyrad_log.txt found an error in step2; see ipyrad_log.txt found an error in step2; see ipyrad_log.txt
Encountered an unexpected error (see ./ipyrad_log.txt) Error message is below ------------------------------- Cannot convert non-finite values (NA or inf) to integer
I'm not sure what the error is, because the ipyrad_log generated is empty. I'm also not sure where the non-finite values would come from, unless they are Ns in the sequences themselves...can't see why it wouldn't be able to handle that though. Here's my params file for reference:
[caan8813@shas0137 data]$ less params-data8.txt
ddrad ## [7] [datatype]: Datatype (see docs): rad, gbs, ddrad, etc. AATTC, TAA ## [8] [restriction_overhang]: Restriction overhang (cut1,) or (cut1, cut2) 5 ## [9] [max_low_qual_bases]: Max low quality base calls (Q<20) in a read 33 ## [10] [phred_Qscore_offset]: phred Q score offset (33 is default and very standard) 6 ## [11] [mindepth_statistical]: Min depth for statistical base calling 2 ## [12] [mindepth_majrule]: Min depth for majority-rule base calling 10000 ## [13] [maxdepth]: Max cluster depth within samples 0.85 ## [14] [clust_threshold]: Clustering threshold for de novo assembly 0 ## [15] [max_barcode_mismatch]: Max number of allowable mismatches in barcodes 0 ## [16] [filter_adapters]: Filter for adapters/primers (1 or 2=stricter) 35 ## [17] [filter_min_trim_len]: Min length of reads after adapter trim 2 ## [18] [max_alleles_consens]: Max alleles per site in consensus sequences 5, 5 ## [19] [max_Ns_consens]: Max N's (uncalled bases) in consensus (R1, R2) 8, 8 ## [20] [max_Hs_consens]: Max Hs (heterozygotes) in consensus (R1, R2) 4 ## [21] [min_samples_locus]: Min # samples per locus for output 100, 100 ## [22] [max_SNPs_locus]: Max # SNPs per locus (R1, R2) 100, 100 ## [23] [max_Indels_locus]: Max # of indels per locus (R1, R2) 0.5 ## [24] [max_shared_Hs_locus]: Max # heterozygous sites per locus (R1, R2) 0, 0 ## [25] [edit_cutsites]: Edit cut-sites (R1, R2) (see docs) 0, 0, 0, 0 ## [26] [trim_overhang]: Trim overhang (see docs) (R1>, <R1, R2>, <R2) p, s, u, n, v ## [27] [output_formats]: Output formats (see docs)
[28] [pop_assign_file]: Path to population assignment file
Any help is much appreciated!