[2024-01-24 12:21:58,733] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:58,735] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:58,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg0324f930-810e-4c66-914e-babb2842b27e/dqc_reference
[2024-01-24 12:22:00,097] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:00,100] [INFO] Task started: Prodigal
[2024-01-24 12:22:00,101] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa8668a4-f206-46b6-a36c-ecca458197e9/GCF_000152145.1_ASM15214v1_genomic.fna.gz | prodigal -d GCF_000152145.1_ASM15214v1_genomic.fna/cds.fna -a GCF_000152145.1_ASM15214v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:14,179] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:14,179] [INFO] Task started: HMMsearch
[2024-01-24 12:22:14,179] [INFO] Running command: hmmsearch --tblout GCF_000152145.1_ASM15214v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0324f930-810e-4c66-914e-babb2842b27e/dqc_reference/reference_markers.hmm GCF_000152145.1_ASM15214v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:14,548] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:14,550] [INFO] Found 6/6 markers.
[2024-01-24 12:22:14,586] [INFO] Query marker FASTA was written to GCF_000152145.1_ASM15214v1_genomic.fna/markers.fasta
[2024-01-24 12:22:14,586] [INFO] Task started: Blastn
[2024-01-24 12:22:14,586] [INFO] Running command: blastn -query GCF_000152145.1_ASM15214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0324f930-810e-4c66-914e-babb2842b27e/dqc_reference/reference_markers.fasta -out GCF_000152145.1_ASM15214v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:15,254] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:15,260] [INFO] Selected 16 target genomes.
[2024-01-24 12:22:15,260] [INFO] Target genome list was writen to GCF_000152145.1_ASM15214v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:15,267] [INFO] Task started: fastANI
[2024-01-24 12:22:15,267] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa8668a4-f206-46b6-a36c-ecca458197e9/GCF_000152145.1_ASM15214v1_genomic.fna.gz --refList GCF_000152145.1_ASM15214v1_genomic.fna/target_genomes.txt --output GCF_000152145.1_ASM15214v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:31,252] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:31,253] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0324f930-810e-4c66-914e-babb2842b27e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:31,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0324f930-810e-4c66-914e-babb2842b27e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:31,260] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:31,260] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:31,260] [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
Oscillochloris trichoides	strain=DG-6	GCA_000152145.1	104176	104176	type	True	99.9998	1453	1454	95	conclusive
Chloroflexus aggregans	strain=DSM 9485	GCA_000021945.1	152260	152260	type	True	76.2989	78	1454	95	below_threshold
Chloroflexus islandicus	strain=isl-2	GCA_001650695.1	1707952	1707952	type	True	76.1887	160	1454	95	below_threshold
Chloroflexus aurantiacus	strain=J-10-fl	GCA_000018865.1	1108	1108	type	True	76.0877	86	1454	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:31,262] [INFO] DFAST Taxonomy check result was written to GCF_000152145.1_ASM15214v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:31,262] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:31,263] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:31,263] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0324f930-810e-4c66-914e-babb2842b27e/dqc_reference/checkm_data
[2024-01-24 12:22:31,264] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:31,307] [INFO] Task started: CheckM
[2024-01-24 12:22:31,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000152145.1_ASM15214v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000152145.1_ASM15214v1_genomic.fna/checkm_input GCF_000152145.1_ASM15214v1_genomic.fna/checkm_result
[2024-01-24 12:23:15,443] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:15,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:15,465] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:15,466] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:15,466] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000152145.1_ASM15214v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:15,466] [INFO] Task started: Blastn
[2024-01-24 12:23:15,467] [INFO] Running command: blastn -query GCF_000152145.1_ASM15214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0324f930-810e-4c66-914e-babb2842b27e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000152145.1_ASM15214v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:16,289] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:16,293] [INFO] Selected 9 target genomes.
[2024-01-24 12:23:16,293] [INFO] Target genome list was writen to GCF_000152145.1_ASM15214v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:16,318] [INFO] Task started: fastANI
[2024-01-24 12:23:16,319] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa8668a4-f206-46b6-a36c-ecca458197e9/GCF_000152145.1_ASM15214v1_genomic.fna.gz --refList GCF_000152145.1_ASM15214v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000152145.1_ASM15214v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:27,286] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:27,298] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:27,298] [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_000152145.1	s__Oscillochloris trichoides	99.9998	1453	1454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004138135.1	s__Oscillochloris fontis	86.6218	1147	1454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903877945.1	s__Oscillochloris sp903877945	77.8566	301	1454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	98.99	98.27	0.81	0.73	10	-
GCA_004138175.2	s__Oscillochloris sp004138175	77.8509	506	1454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887465.1	s__Oscillochloris sp903887465	77.8124	368	1454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	99.82	99.74	0.95	0.93	6	-
GCA_903920315.1	s__Oscillochloris sp903920315	77.4544	311	1454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	98.25	98.25	0.71	0.71	2	-
GCA_013388805.1	s__JACAEO01 sp013388805	76.6022	238	1454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__JACAEO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002532075.1	s__Chloroploca asiatica	76.2743	132	1454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Chloroploca	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004367505.1	s__OHK40 sp004367505	76.2269	217	1454	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__OHK40	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:27,300] [INFO] GTDB search result was written to GCF_000152145.1_ASM15214v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:27,301] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:27,304] [INFO] DFAST_QC result json was written to GCF_000152145.1_ASM15214v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:27,305] [INFO] DFAST_QC completed!
[2024-01-24 12:23:27,305] [INFO] Total running time: 0h1m29s