[2023-03-17 08:11:32,453] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:11:32,453] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:11:32,453] [INFO] DQC Reference Directory: /var/lib/cwl/stg70650674-770f-4713-aff5-f0eb71359409/dqc_reference
[2023-03-17 08:11:33,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:11:33,598] [INFO] Task started: Prodigal
[2023-03-17 08:11:33,598] [INFO] Running command: cat /var/lib/cwl/stgbdaaf97e-d0b0-44d4-bb11-272ba934f6d9/OceanDNA-b34273.fa | prodigal -d OceanDNA-b34273/cds.fna -a OceanDNA-b34273/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:11:42,066] [INFO] Task succeeded: Prodigal
[2023-03-17 08:11:42,067] [INFO] Task started: HMMsearch
[2023-03-17 08:11:42,067] [INFO] Running command: hmmsearch --tblout OceanDNA-b34273/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70650674-770f-4713-aff5-f0eb71359409/dqc_reference/reference_markers.hmm OceanDNA-b34273/protein.faa > /dev/null
[2023-03-17 08:11:42,245] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:11:42,245] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgbdaaf97e-d0b0-44d4-bb11-272ba934f6d9/OceanDNA-b34273.fa]
[2023-03-17 08:11:42,263] [INFO] Query marker FASTA was written to OceanDNA-b34273/markers.fasta
[2023-03-17 08:11:42,263] [INFO] Task started: Blastn
[2023-03-17 08:11:42,263] [INFO] Running command: blastn -query OceanDNA-b34273/markers.fasta -db /var/lib/cwl/stg70650674-770f-4713-aff5-f0eb71359409/dqc_reference/reference_markers.fasta -out OceanDNA-b34273/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:11:42,759] [INFO] Task succeeded: Blastn
[2023-03-17 08:11:42,759] [INFO] Selected 19 target genomes.
[2023-03-17 08:11:42,760] [INFO] Target genome list was writen to OceanDNA-b34273/target_genomes.txt
[2023-03-17 08:11:42,770] [INFO] Task started: fastANI
[2023-03-17 08:11:42,770] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdaaf97e-d0b0-44d4-bb11-272ba934f6d9/OceanDNA-b34273.fa --refList OceanDNA-b34273/target_genomes.txt --output OceanDNA-b34273/fastani_result.tsv --threads 1
[2023-03-17 08:11:55,483] [INFO] Task succeeded: fastANI
[2023-03-17 08:11:55,483] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70650674-770f-4713-aff5-f0eb71359409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:11:55,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70650674-770f-4713-aff5-f0eb71359409/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:11:55,489] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:11:55,489] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 08:11:55,489] [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
Thalassotalea algicola	strain=M1531	GCA_012932965.1	2716224	2716224	type	True	77.3863	66	479	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	77.3815	61	479	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.1974	62	479	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	76.8688	50	479	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	76.3343	51	479	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	76.3042	50	479	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:11:55,489] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34273/tc_result.tsv
[2023-03-17 08:11:55,489] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:11:55,489] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:11:55,489] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70650674-770f-4713-aff5-f0eb71359409/dqc_reference/checkm_data
[2023-03-17 08:11:55,490] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:11:55,503] [INFO] Task started: CheckM
[2023-03-17 08:11:55,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34273/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34273/checkm_input OceanDNA-b34273/checkm_result
[2023-03-17 08:12:22,033] [INFO] Task succeeded: CheckM
[2023-03-17 08:12:22,033] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 08:12:22,035] [INFO] ===== Completeness check finished =====
[2023-03-17 08:12:22,036] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:12:22,036] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34273/markers.fasta)
[2023-03-17 08:12:22,037] [INFO] Task started: Blastn
[2023-03-17 08:12:22,037] [INFO] Running command: blastn -query OceanDNA-b34273/markers.fasta -db /var/lib/cwl/stg70650674-770f-4713-aff5-f0eb71359409/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34273/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:12:22,671] [INFO] Task succeeded: Blastn
[2023-03-17 08:12:22,672] [INFO] Selected 14 target genomes.
[2023-03-17 08:12:22,672] [INFO] Target genome list was writen to OceanDNA-b34273/target_genomes_gtdb.txt
[2023-03-17 08:12:22,810] [INFO] Task started: fastANI
[2023-03-17 08:12:22,810] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdaaf97e-d0b0-44d4-bb11-272ba934f6d9/OceanDNA-b34273.fa --refList OceanDNA-b34273/target_genomes_gtdb.txt --output OceanDNA-b34273/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:12:32,122] [INFO] Task succeeded: fastANI
[2023-03-17 08:12:32,127] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:12:32,127] [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_014898095.1	s__Thalassotalea sp014898095	78.9322	147	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390395.1	s__Thalassotalea euphylliae_C	77.6533	71	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390335.1	s__Thalassotalea euphylliae_B	77.5454	73	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390375.1	s__Thalassotalea euphylliae_A	77.5196	69	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932965.1	s__Thalassotalea algicola	77.3863	66	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207645.1	s__Thalassotalea_B piscium	76.2495	50	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	76.1006	52	479	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:12:32,127] [INFO] GTDB search result was written to OceanDNA-b34273/result_gtdb.tsv
[2023-03-17 08:12:32,128] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:12:32,129] [INFO] DFAST_QC result json was written to OceanDNA-b34273/dqc_result.json
[2023-03-17 08:12:32,129] [INFO] DFAST_QC completed!
[2023-03-17 08:12:32,129] [INFO] Total running time: 0h0m60s