[2023-03-15 03:25:37,041] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:25:37,041] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:25:37,041] [INFO] DQC Reference Directory: /var/lib/cwl/stgce2e6c93-66e0-4f66-b29b-cb2331505ca7/dqc_reference
[2023-03-15 03:25:38,140] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:25:38,141] [INFO] Task started: Prodigal
[2023-03-15 03:25:38,141] [INFO] Running command: cat /var/lib/cwl/stg4553cb84-a5cd-4e42-94a0-5ce889abe1c8/OceanDNA-b16039.fa | prodigal -d OceanDNA-b16039/cds.fna -a OceanDNA-b16039/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:26:16,530] [INFO] Task succeeded: Prodigal
[2023-03-15 03:26:16,531] [INFO] Task started: HMMsearch
[2023-03-15 03:26:16,531] [INFO] Running command: hmmsearch --tblout OceanDNA-b16039/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce2e6c93-66e0-4f66-b29b-cb2331505ca7/dqc_reference/reference_markers.hmm OceanDNA-b16039/protein.faa > /dev/null
[2023-03-15 03:26:16,861] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:26:16,862] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4553cb84-a5cd-4e42-94a0-5ce889abe1c8/OceanDNA-b16039.fa]
[2023-03-15 03:26:16,902] [INFO] Query marker FASTA was written to OceanDNA-b16039/markers.fasta
[2023-03-15 03:26:16,903] [INFO] Task started: Blastn
[2023-03-15 03:26:16,903] [INFO] Running command: blastn -query OceanDNA-b16039/markers.fasta -db /var/lib/cwl/stgce2e6c93-66e0-4f66-b29b-cb2331505ca7/dqc_reference/reference_markers.fasta -out OceanDNA-b16039/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:26:17,408] [INFO] Task succeeded: Blastn
[2023-03-15 03:26:17,410] [INFO] Selected 16 target genomes.
[2023-03-15 03:26:17,410] [INFO] Target genome list was writen to OceanDNA-b16039/target_genomes.txt
[2023-03-15 03:26:17,419] [INFO] Task started: fastANI
[2023-03-15 03:26:17,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg4553cb84-a5cd-4e42-94a0-5ce889abe1c8/OceanDNA-b16039.fa --refList OceanDNA-b16039/target_genomes.txt --output OceanDNA-b16039/fastani_result.tsv --threads 1
[2023-03-15 03:26:45,509] [INFO] Task succeeded: fastANI
[2023-03-15 03:26:45,510] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce2e6c93-66e0-4f66-b29b-cb2331505ca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:26:45,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce2e6c93-66e0-4f66-b29b-cb2331505ca7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:26:45,518] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:26:45,518] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:26:45,518] [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
Moorena producens	strain=3L	GCA_000211815.1	1155739	1155739	type	True	92.8576	1942	2412	95	below_threshold
Moorena producens	strain=3L	GCA_001942475.1	1155739	1155739	type	True	92.7646	1985	2412	95	below_threshold
Allocoleopsis franciscana	strain=PCC 7113	GCA_000317515.1	2886352	2886352	type	True	76.1091	212	2412	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	75.5815	74	2412	95	below_threshold
Oscillatoria acuminata	strain=PCC 6304	GCA_000317105.1	118323	118323	type	True	75.5091	60	2412	95	below_threshold
Argonema galeatum	strain=A003/A1	GCA_023333595.1	2942762	2942762	type	True	75.4397	90	2412	95	below_threshold
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	75.4394	91	2412	95	below_threshold
Kovacikia minuta	strain=CCNU0001	GCA_020091585.1	2931930	2931930	type	True	75.3437	60	2412	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	75.2771	99	2412	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	75.077	83	2412	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	75.0715	84	2412	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:26:45,519] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16039/tc_result.tsv
[2023-03-15 03:26:45,519] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:26:45,519] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:26:45,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce2e6c93-66e0-4f66-b29b-cb2331505ca7/dqc_reference/checkm_data
[2023-03-15 03:26:45,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:26:45,529] [INFO] Task started: CheckM
[2023-03-15 03:26:45,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16039/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16039/checkm_input OceanDNA-b16039/checkm_result
[2023-03-15 03:28:16,642] [INFO] Task succeeded: CheckM
[2023-03-15 03:28:16,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:28:16,647] [INFO] ===== Completeness check finished =====
[2023-03-15 03:28:16,647] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:28:16,648] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16039/markers.fasta)
[2023-03-15 03:28:16,648] [INFO] Task started: Blastn
[2023-03-15 03:28:16,648] [INFO] Running command: blastn -query OceanDNA-b16039/markers.fasta -db /var/lib/cwl/stgce2e6c93-66e0-4f66-b29b-cb2331505ca7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16039/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:28:17,333] [INFO] Task succeeded: Blastn
[2023-03-15 03:28:17,334] [INFO] Selected 7 target genomes.
[2023-03-15 03:28:17,335] [INFO] Target genome list was writen to OceanDNA-b16039/target_genomes_gtdb.txt
[2023-03-15 03:28:17,344] [INFO] Task started: fastANI
[2023-03-15 03:28:17,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg4553cb84-a5cd-4e42-94a0-5ce889abe1c8/OceanDNA-b16039.fa --refList OceanDNA-b16039/target_genomes_gtdb.txt --output OceanDNA-b16039/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:29:12,577] [INFO] Task succeeded: fastANI
[2023-03-15 03:29:12,583] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:29:12,583] [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_001767235.1	s__Moorea producens_A	93.4892	2122	2412	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	96.04	96.04	0.84	0.84	2	-
GCF_001942495.1	s__Moorea bouillonii	93.3518	2002	2412	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	96.52	96.51	0.86	0.86	3	-
GCA_010692325.1	s__Moorea sp010692325	93.331	1790	2412	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	97.88	97.68	0.88	0.86	3	-
GCA_010671925.1	s__Moorea sp010671925	93.2708	2138	2412	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010692395.1	s__Moorea sp010692395	93.1679	1789	2412	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524395.1	s__Moorea sp011524395	93.0556	1820	2412	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000211815.1	s__Moorea producens	92.8363	1946	2412	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	98.41	95.37	0.92	0.86	6	-
--------------------------------------------------------------------------------
[2023-03-15 03:29:12,584] [INFO] GTDB search result was written to OceanDNA-b16039/result_gtdb.tsv
[2023-03-15 03:29:12,585] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:29:12,588] [INFO] DFAST_QC result json was written to OceanDNA-b16039/dqc_result.json
[2023-03-15 03:29:12,588] [INFO] DFAST_QC completed!
[2023-03-15 03:29:12,588] [INFO] Total running time: 0h3m36s