[2024-01-24 14:19:59,561] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:59,563] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:59,563] [INFO] DQC Reference Directory: /var/lib/cwl/stgdca7f348-d94f-41ea-88a4-aad4ff4f6e18/dqc_reference
[2024-01-24 14:20:01,088] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:01,089] [INFO] Task started: Prodigal
[2024-01-24 14:20:01,089] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1d62f4b-05a4-462b-81ef-5d9310e2eeaf/GCF_000021945.1_ASM2194v1_genomic.fna.gz | prodigal -d GCF_000021945.1_ASM2194v1_genomic.fna/cds.fna -a GCF_000021945.1_ASM2194v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:17,750] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:17,750] [INFO] Task started: HMMsearch
[2024-01-24 14:20:17,750] [INFO] Running command: hmmsearch --tblout GCF_000021945.1_ASM2194v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdca7f348-d94f-41ea-88a4-aad4ff4f6e18/dqc_reference/reference_markers.hmm GCF_000021945.1_ASM2194v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:18,085] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:18,086] [INFO] Found 6/6 markers.
[2024-01-24 14:20:18,132] [INFO] Query marker FASTA was written to GCF_000021945.1_ASM2194v1_genomic.fna/markers.fasta
[2024-01-24 14:20:18,132] [INFO] Task started: Blastn
[2024-01-24 14:20:18,133] [INFO] Running command: blastn -query GCF_000021945.1_ASM2194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdca7f348-d94f-41ea-88a4-aad4ff4f6e18/dqc_reference/reference_markers.fasta -out GCF_000021945.1_ASM2194v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:18,764] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:18,768] [INFO] Selected 12 target genomes.
[2024-01-24 14:20:18,769] [INFO] Target genome list was writen to GCF_000021945.1_ASM2194v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:18,781] [INFO] Task started: fastANI
[2024-01-24 14:20:18,782] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1d62f4b-05a4-462b-81ef-5d9310e2eeaf/GCF_000021945.1_ASM2194v1_genomic.fna.gz --refList GCF_000021945.1_ASM2194v1_genomic.fna/target_genomes.txt --output GCF_000021945.1_ASM2194v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:27,683] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:27,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdca7f348-d94f-41ea-88a4-aad4ff4f6e18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:27,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdca7f348-d94f-41ea-88a4-aad4ff4f6e18/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:27,690] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:27,690] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:27,690] [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
Chloroflexus aggregans	strain=DSM 9485	GCA_000021945.1	152260	152260	type	True	100.0	1561	1561	95	conclusive
Roseiflexus castenholzii	strain=DSM 13941	GCA_000017805.1	120962	120962	type	True	82.4938	112	1561	95	below_threshold
Chloroflexus islandicus	strain=isl-2	GCA_001650695.1	1707952	1707952	type	True	81.0758	822	1561	95	below_threshold
Chloroflexus aurantiacus	strain=J-10-fl	GCA_000018865.1	1108	1108	type	True	77.8025	472	1561	95	below_threshold
Oscillochloris trichoides	strain=DG-6	GCA_000152145.1	104176	104176	type	True	76.1136	82	1561	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:27,692] [INFO] DFAST Taxonomy check result was written to GCF_000021945.1_ASM2194v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:27,692] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:27,692] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:27,693] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdca7f348-d94f-41ea-88a4-aad4ff4f6e18/dqc_reference/checkm_data
[2024-01-24 14:20:27,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:27,741] [INFO] Task started: CheckM
[2024-01-24 14:20:27,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000021945.1_ASM2194v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000021945.1_ASM2194v1_genomic.fna/checkm_input GCF_000021945.1_ASM2194v1_genomic.fna/checkm_result
[2024-01-24 14:21:18,272] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:18,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:18,299] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:18,300] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:18,300] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000021945.1_ASM2194v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:18,301] [INFO] Task started: Blastn
[2024-01-24 14:21:18,301] [INFO] Running command: blastn -query GCF_000021945.1_ASM2194v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdca7f348-d94f-41ea-88a4-aad4ff4f6e18/dqc_reference/reference_markers_gtdb.fasta -out GCF_000021945.1_ASM2194v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:19,062] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:19,066] [INFO] Selected 11 target genomes.
[2024-01-24 14:21:19,066] [INFO] Target genome list was writen to GCF_000021945.1_ASM2194v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:19,086] [INFO] Task started: fastANI
[2024-01-24 14:21:19,086] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1d62f4b-05a4-462b-81ef-5d9310e2eeaf/GCF_000021945.1_ASM2194v1_genomic.fna.gz --refList GCF_000021945.1_ASM2194v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000021945.1_ASM2194v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:29,018] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:29,032] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:29,032] [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_000021945.1	s__Chloroflexus aggregans	100.0	1561	1561	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Chloroflexus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001650695.1	s__Chloroflexus islandicus	81.0755	823	1561	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Chloroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018865.1	s__Chloroflexus aurantiacus	77.8152	470	1561	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Chloroflexus	95.0	99.51	98.60	0.98	0.95	7	-
GCF_000516515.1	s__Chloroflexus sp000516515	77.4585	368	1561	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Chloroflexus	95.0	95.29	95.23	0.95	0.93	3	-
GCF_000735195.1	s__Chloroflexus sp000735195	77.2009	365	1561	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Chloroflexus	95.0	96.40	95.13	0.90	0.88	5	-
GCA_012032775.1	s__JAAUQO01 sp012032775	75.9512	116	1561	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__JAAUQO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903877945.1	s__Oscillochloris sp903877945	75.7746	55	1561	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	98.99	98.27	0.81	0.73	10	-
GCA_004367505.1	s__OHK40 sp004367505	75.6195	87	1561	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__OHK40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903920315.1	s__Oscillochloris sp903920315	75.5254	68	1561	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	98.25	98.25	0.71	0.71	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:29,034] [INFO] GTDB search result was written to GCF_000021945.1_ASM2194v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:29,034] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:29,037] [INFO] DFAST_QC result json was written to GCF_000021945.1_ASM2194v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:29,037] [INFO] DFAST_QC completed!
[2024-01-24 14:21:29,037] [INFO] Total running time: 0h1m29s