[2023-03-18 03:27:00,945] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,954] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,954] [INFO] DQC Reference Directory: /var/lib/cwl/stg79c355af-cab2-49b4-b515-2a2f481af42d/dqc_reference
[2023-03-18 03:27:02,635] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:02,636] [INFO] Task started: Prodigal
[2023-03-18 03:27:02,636] [INFO] Running command: cat /var/lib/cwl/stg6fe33863-a637-4359-babe-75f255a017a4/OceanDNA-a2656.fa | prodigal -d OceanDNA-a2656/cds.fna -a OceanDNA-a2656/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:09,114] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:09,115] [INFO] Task started: HMMsearch
[2023-03-18 03:27:09,115] [INFO] Running command: hmmsearch --tblout OceanDNA-a2656/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79c355af-cab2-49b4-b515-2a2f481af42d/dqc_reference/reference_markers.hmm OceanDNA-a2656/protein.faa > /dev/null
[2023-03-18 03:27:09,273] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:09,274] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6fe33863-a637-4359-babe-75f255a017a4/OceanDNA-a2656.fa]
[2023-03-18 03:27:09,283] [INFO] Query marker FASTA was written to OceanDNA-a2656/markers.fasta
[2023-03-18 03:27:09,284] [INFO] Task started: Blastn
[2023-03-18 03:27:09,284] [INFO] Running command: blastn -query OceanDNA-a2656/markers.fasta -db /var/lib/cwl/stg79c355af-cab2-49b4-b515-2a2f481af42d/dqc_reference/reference_markers.fasta -out OceanDNA-a2656/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:09,706] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:09,706] [INFO] Selected 5 target genomes.
[2023-03-18 03:27:09,707] [INFO] Target genome list was writen to OceanDNA-a2656/target_genomes.txt
[2023-03-18 03:27:09,709] [INFO] Task started: fastANI
[2023-03-18 03:27:09,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fe33863-a637-4359-babe-75f255a017a4/OceanDNA-a2656.fa --refList OceanDNA-a2656/target_genomes.txt --output OceanDNA-a2656/fastani_result.tsv --threads 1
[2023-03-18 03:27:13,163] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:13,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79c355af-cab2-49b4-b515-2a2f481af42d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:13,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79c355af-cab2-49b4-b515-2a2f481af42d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:13,164] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:27:13,164] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:27:13,164] [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
--------------------------------------------------------------------------------
[2023-03-18 03:27:13,164] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2656/tc_result.tsv
[2023-03-18 03:27:13,164] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:13,164] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:13,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79c355af-cab2-49b4-b515-2a2f481af42d/dqc_reference/checkm_data
[2023-03-18 03:27:13,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:13,170] [INFO] Task started: CheckM
[2023-03-18 03:27:13,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2656/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2656/checkm_input OceanDNA-a2656/checkm_result
[2023-03-18 03:27:35,438] [INFO] Task succeeded: CheckM
[2023-03-18 03:27:35,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:27:35,440] [INFO] ===== Completeness check finished =====
[2023-03-18 03:27:35,441] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:27:35,441] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2656/markers.fasta)
[2023-03-18 03:27:35,441] [INFO] Task started: Blastn
[2023-03-18 03:27:35,441] [INFO] Running command: blastn -query OceanDNA-a2656/markers.fasta -db /var/lib/cwl/stg79c355af-cab2-49b4-b515-2a2f481af42d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2656/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:35,876] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:35,877] [INFO] Selected 8 target genomes.
[2023-03-18 03:27:35,877] [INFO] Target genome list was writen to OceanDNA-a2656/target_genomes_gtdb.txt
[2023-03-18 03:27:35,885] [INFO] Task started: fastANI
[2023-03-18 03:27:35,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fe33863-a637-4359-babe-75f255a017a4/OceanDNA-a2656.fa --refList OceanDNA-a2656/target_genomes_gtdb.txt --output OceanDNA-a2656/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:27:38,109] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:38,114] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:27:38,115] [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
GCA_002722615.1	s__MGIIa-L2 sp002722615	80.9173	208	328	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	97.14	95.81	0.83	0.81	4	-
GCA_013911465.1	s__MGIIa-L2 sp013911465	79.4361	168	328	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706065.1	s__MGIIa-L2 sp002706065	78.6134	143	328	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002502215.1	s__MGIIa-L2 sp002502215	78.3038	138	328	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	98.03	97.17	0.84	0.82	4	-
GCA_018623995.1	s__MGIIa-L2 sp018623995	78.0954	122	328	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692685.1	s__MGIIa-L2 sp002692685	77.8687	70	328	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698145.1	s__MGIIa-L2 sp002698145	77.8271	130	328	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	98.10	97.13	0.94	0.83	7	-
GCA_002171315.2	s__MGIIa-L2 sp002171315	76.9638	55	328	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:27:38,115] [INFO] GTDB search result was written to OceanDNA-a2656/result_gtdb.tsv
[2023-03-18 03:27:38,115] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:27:38,116] [INFO] DFAST_QC result json was written to OceanDNA-a2656/dqc_result.json
[2023-03-18 03:27:38,116] [INFO] DFAST_QC completed!
[2023-03-18 03:27:38,116] [INFO] Total running time: 0h0m37s