[2023-03-15 07:58:33,369] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:58:33,370] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:58:33,370] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd335ac6-b9bf-4573-8773-c1646017df9f/dqc_reference
[2023-03-15 07:58:35,137] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:58:35,137] [INFO] Task started: Prodigal
[2023-03-15 07:58:35,137] [INFO] Running command: cat /var/lib/cwl/stg5a1a7f96-dfb1-40c5-b138-d78049e5374d/OceanDNA-b26879.fa | prodigal -d OceanDNA-b26879/cds.fna -a OceanDNA-b26879/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:59:02,378] [INFO] Task succeeded: Prodigal
[2023-03-15 07:59:02,378] [INFO] Task started: HMMsearch
[2023-03-15 07:59:02,378] [INFO] Running command: hmmsearch --tblout OceanDNA-b26879/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd335ac6-b9bf-4573-8773-c1646017df9f/dqc_reference/reference_markers.hmm OceanDNA-b26879/protein.faa > /dev/null
[2023-03-15 07:59:02,598] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:59:02,598] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5a1a7f96-dfb1-40c5-b138-d78049e5374d/OceanDNA-b26879.fa]
[2023-03-15 07:59:02,659] [INFO] Query marker FASTA was written to OceanDNA-b26879/markers.fasta
[2023-03-15 07:59:02,660] [INFO] Task started: Blastn
[2023-03-15 07:59:02,660] [INFO] Running command: blastn -query OceanDNA-b26879/markers.fasta -db /var/lib/cwl/stgdd335ac6-b9bf-4573-8773-c1646017df9f/dqc_reference/reference_markers.fasta -out OceanDNA-b26879/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:59:03,554] [INFO] Task succeeded: Blastn
[2023-03-15 07:59:03,560] [INFO] Selected 11 target genomes.
[2023-03-15 07:59:03,560] [INFO] Target genome list was writen to OceanDNA-b26879/target_genomes.txt
[2023-03-15 07:59:03,566] [INFO] Task started: fastANI
[2023-03-15 07:59:03,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a1a7f96-dfb1-40c5-b138-d78049e5374d/OceanDNA-b26879.fa --refList OceanDNA-b26879/target_genomes.txt --output OceanDNA-b26879/fastani_result.tsv --threads 1
[2023-03-15 07:59:14,310] [INFO] Task succeeded: fastANI
[2023-03-15 07:59:14,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd335ac6-b9bf-4573-8773-c1646017df9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:59:14,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd335ac6-b9bf-4573-8773-c1646017df9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:59:14,318] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2023-03-15 07:59:14,318] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 07:59:14,318] [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
Martelella mediterranea	strain=DSM 17316	GCA_000376125.1	293089	293089	type	True	96.1191	1285	1483	95	conclusive
Martelella mediterranea	strain=MACL11	GCA_002043005.1	293089	293089	type	True	96.0242	1312	1483	95	conclusive
Martelella limonii	strain=NBRC 109441	GCA_013344475.1	1647649	1647649	type	True	84.8666	897	1483	95	below_threshold
Martelella endophytica	strain=YC6887	GCA_000960975.1	1486262	1486262	type	True	83.2556	768	1483	95	below_threshold
Martelella lutilitoris	strain=GH2-6	GCA_005924265.1	2583532	2583532	type	True	83.1939	803	1483	95	below_threshold
Martelella radicis	strain=DSM 28101	GCA_014196625.1	1397476	1397476	type	True	83.0981	808	1483	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.8596	453	1483	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	78.5914	443	1483	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.4038	355	1483	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	77.1998	230	1483	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	77.1835	231	1483	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:59:14,320] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26879/tc_result.tsv
[2023-03-15 07:59:14,323] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:59:14,323] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:59:14,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd335ac6-b9bf-4573-8773-c1646017df9f/dqc_reference/checkm_data
[2023-03-15 07:59:14,324] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:59:14,332] [INFO] Task started: CheckM
[2023-03-15 07:59:14,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26879/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26879/checkm_input OceanDNA-b26879/checkm_result
[2023-03-15 08:00:20,667] [INFO] Task succeeded: CheckM
[2023-03-15 08:00:20,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:00:20,798] [INFO] ===== Completeness check finished =====
[2023-03-15 08:00:20,798] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:00:20,799] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26879/markers.fasta)
[2023-03-15 08:00:20,800] [INFO] Task started: Blastn
[2023-03-15 08:00:20,800] [INFO] Running command: blastn -query OceanDNA-b26879/markers.fasta -db /var/lib/cwl/stgdd335ac6-b9bf-4573-8773-c1646017df9f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26879/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:00:22,596] [INFO] Task succeeded: Blastn
[2023-03-15 08:00:22,605] [INFO] Selected 8 target genomes.
[2023-03-15 08:00:22,605] [INFO] Target genome list was writen to OceanDNA-b26879/target_genomes_gtdb.txt
[2023-03-15 08:00:22,616] [INFO] Task started: fastANI
[2023-03-15 08:00:22,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a1a7f96-dfb1-40c5-b138-d78049e5374d/OceanDNA-b26879.fa --refList OceanDNA-b26879/target_genomes_gtdb.txt --output OceanDNA-b26879/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:00:31,763] [INFO] Task succeeded: fastANI
[2023-03-15 08:00:31,768] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:00:31,768] [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_002043005.1	s__Martelella mediterranea	96.0405	1311	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	97.32	95.96	0.90	0.83	4	conclusive
GCF_013459645.1	s__Martelella sp013459645	88.657	1097	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013344475.1	s__Martelella limonii	84.8492	899	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001578105.1	s__Martelella sp001578105	83.8849	883	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	97.55	95.11	0.93	0.87	3	-
GCF_000960975.1	s__Martelella endophytica	83.2378	769	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005924265.1	s__Martelella lutilitoris	83.1808	804	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196625.1	s__Martelella radicis	83.1222	806	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003001975.1	s__Martelella mediterranea_A	82.3308	745	1483	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:00:31,770] [INFO] GTDB search result was written to OceanDNA-b26879/result_gtdb.tsv
[2023-03-15 08:00:31,776] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:00:31,780] [INFO] DFAST_QC result json was written to OceanDNA-b26879/dqc_result.json
[2023-03-15 08:00:31,780] [INFO] DFAST_QC completed!
[2023-03-15 08:00:31,780] [INFO] Total running time: 0h1m58s