[2023-03-18 23:44:06,381] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,381] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,381] [INFO] DQC Reference Directory: /var/lib/cwl/stg4448376e-d21c-400e-94b9-e636ca5d7038/dqc_reference
[2023-03-18 23:44:07,521] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,522] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,522] [INFO] Running command: cat /var/lib/cwl/stgeb276ce1-c501-40be-8e04-1a420d0b9845/OceanDNA-b35282.fa | prodigal -d OceanDNA-b35282/cds.fna -a OceanDNA-b35282/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:28,144] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:28,144] [INFO] Task started: HMMsearch
[2023-03-18 23:44:28,144] [INFO] Running command: hmmsearch --tblout OceanDNA-b35282/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4448376e-d21c-400e-94b9-e636ca5d7038/dqc_reference/reference_markers.hmm OceanDNA-b35282/protein.faa > /dev/null
[2023-03-18 23:44:28,358] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:28,359] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeb276ce1-c501-40be-8e04-1a420d0b9845/OceanDNA-b35282.fa]
[2023-03-18 23:44:28,383] [INFO] Query marker FASTA was written to OceanDNA-b35282/markers.fasta
[2023-03-18 23:44:28,385] [INFO] Task started: Blastn
[2023-03-18 23:44:28,385] [INFO] Running command: blastn -query OceanDNA-b35282/markers.fasta -db /var/lib/cwl/stg4448376e-d21c-400e-94b9-e636ca5d7038/dqc_reference/reference_markers.fasta -out OceanDNA-b35282/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:28,962] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:28,963] [INFO] Selected 12 target genomes.
[2023-03-18 23:44:28,963] [INFO] Target genome list was writen to OceanDNA-b35282/target_genomes.txt
[2023-03-18 23:44:28,972] [INFO] Task started: fastANI
[2023-03-18 23:44:28,972] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb276ce1-c501-40be-8e04-1a420d0b9845/OceanDNA-b35282.fa --refList OceanDNA-b35282/target_genomes.txt --output OceanDNA-b35282/fastani_result.tsv --threads 1
[2023-03-18 23:44:40,420] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:40,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4448376e-d21c-400e-94b9-e636ca5d7038/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:40,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4448376e-d21c-400e-94b9-e636ca5d7038/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:40,429] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 23:44:40,429] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 23:44:40,429] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Shewanella hafniensis	strain=ATCC BAA-1207	GCA_019655335.1	365590	365590	type	True	96.754	1104	1237	95	conclusive
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	94.5077	1141	1237	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	90.7731	1113	1237	95	below_threshold
Shewanella glacialipiscicola	strain=T147	GCA_019655235.1	614069	614069	type	True	84.7922	820	1237	95	below_threshold
Shewanella glacialipiscicola	strain=LMG 23744	GCA_023283485.1	614069	614069	type	True	84.7792	899	1237	95	below_threshold
Shewanella morhuae	strain=ATCC BAA-1205	GCA_900156405.1	365591	365591	type	True	84.4468	920	1237	95	below_threshold
Shewanella putrefaciens	strain=ATCC 8071	GCA_016406325.1	24	24	type	True	84.3948	901	1237	95	below_threshold
Shewanella putrefaciens	strain=JCM 20190	GCA_014647555.1	24	24	type	True	84.388	888	1237	95	below_threshold
Shewanella putrefaciens	strain=NBRC 3908	GCA_001591325.1	24	24	type	True	84.3156	875	1237	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	83.7882	880	1237	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	81.4572	837	1237	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	81.2496	844	1237	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:44:40,436] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35282/tc_result.tsv
[2023-03-18 23:44:40,445] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:40,445] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:40,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4448376e-d21c-400e-94b9-e636ca5d7038/dqc_reference/checkm_data
[2023-03-18 23:44:40,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:40,461] [INFO] Task started: CheckM
[2023-03-18 23:44:40,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35282/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35282/checkm_input OceanDNA-b35282/checkm_result
[2023-03-18 23:45:32,850] [INFO] Task succeeded: CheckM
[2023-03-18 23:45:32,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:45:32,856] [INFO] ===== Completeness check finished =====
[2023-03-18 23:45:32,856] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:45:32,857] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35282/markers.fasta)
[2023-03-18 23:45:32,858] [INFO] Task started: Blastn
[2023-03-18 23:45:32,858] [INFO] Running command: blastn -query OceanDNA-b35282/markers.fasta -db /var/lib/cwl/stg4448376e-d21c-400e-94b9-e636ca5d7038/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35282/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:45:33,640] [INFO] Task succeeded: Blastn
[2023-03-18 23:45:33,641] [INFO] Selected 8 target genomes.
[2023-03-18 23:45:33,642] [INFO] Target genome list was writen to OceanDNA-b35282/target_genomes_gtdb.txt
[2023-03-18 23:45:33,649] [INFO] Task started: fastANI
[2023-03-18 23:45:33,649] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb276ce1-c501-40be-8e04-1a420d0b9845/OceanDNA-b35282.fa --refList OceanDNA-b35282/target_genomes_gtdb.txt --output OceanDNA-b35282/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:45:42,222] [INFO] Task succeeded: fastANI
[2023-03-18 23:45:42,228] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:45:42,228] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002838165.1	s__Shewanella sp002838165	96.9347	1142	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.37	97.32	0.89	0.88	8	conclusive
GCF_900456975.1	s__Shewanella baltica	94.5077	1141	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_002966515.1	s__Shewanella sp002966515	90.8207	1089	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	-
GCA_002783505.1	s__Shewanella sp002783505	85.5923	947	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156405.1	s__Shewanella morhuae	84.4531	919	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
GCF_016406325.1	s__Shewanella putrefaciens	84.4002	900	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.29	98.60	0.96	0.93	12	-
GCF_016406305.1	s__Shewanella putrefaciens_C	84.369	920	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014665.1	s__Shewanella sp000014665	81.4445	852	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.13	97.13	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-18 23:45:42,228] [INFO] GTDB search result was written to OceanDNA-b35282/result_gtdb.tsv
[2023-03-18 23:45:42,228] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:45:42,230] [INFO] DFAST_QC result json was written to OceanDNA-b35282/dqc_result.json
[2023-03-18 23:45:42,230] [INFO] DFAST_QC completed!
[2023-03-18 23:45:42,230] [INFO] Total running time: 0h1m36s