[2024-01-24 13:01:50,129] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:50,132] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:50,133] [INFO] DQC Reference Directory: /var/lib/cwl/stg53dd48c7-58e3-4525-b8d4-1f8596bffb23/dqc_reference
[2024-01-24 13:01:51,411] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:51,412] [INFO] Task started: Prodigal
[2024-01-24 13:01:51,413] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fd24a1a-8210-4f96-87d9-5f9808559a44/GCF_003182595.1_ASM318259v1_genomic.fna.gz | prodigal -d GCF_003182595.1_ASM318259v1_genomic.fna/cds.fna -a GCF_003182595.1_ASM318259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:06,051] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:06,052] [INFO] Task started: HMMsearch
[2024-01-24 13:02:06,052] [INFO] Running command: hmmsearch --tblout GCF_003182595.1_ASM318259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53dd48c7-58e3-4525-b8d4-1f8596bffb23/dqc_reference/reference_markers.hmm GCF_003182595.1_ASM318259v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:06,376] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:06,378] [INFO] Found 6/6 markers.
[2024-01-24 13:02:06,408] [INFO] Query marker FASTA was written to GCF_003182595.1_ASM318259v1_genomic.fna/markers.fasta
[2024-01-24 13:02:06,409] [INFO] Task started: Blastn
[2024-01-24 13:02:06,409] [INFO] Running command: blastn -query GCF_003182595.1_ASM318259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53dd48c7-58e3-4525-b8d4-1f8596bffb23/dqc_reference/reference_markers.fasta -out GCF_003182595.1_ASM318259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:07,010] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:07,015] [INFO] Selected 16 target genomes.
[2024-01-24 13:02:07,015] [INFO] Target genome list was writen to GCF_003182595.1_ASM318259v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:07,036] [INFO] Task started: fastANI
[2024-01-24 13:02:07,036] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fd24a1a-8210-4f96-87d9-5f9808559a44/GCF_003182595.1_ASM318259v1_genomic.fna.gz --refList GCF_003182595.1_ASM318259v1_genomic.fna/target_genomes.txt --output GCF_003182595.1_ASM318259v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:16,968] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:16,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53dd48c7-58e3-4525-b8d4-1f8596bffb23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:16,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53dd48c7-58e3-4525-b8d4-1f8596bffb23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:16,975] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:16,976] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:16,976] [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
Prosthecochloris marina	strain=V1	GCA_003182595.1	2017681	2017681	type	True	100.0	895	896	95	conclusive
Prosthecochloris aestuarii	strain=DSM 271	GCA_000020625.1	1102	1102	type	True	77.6256	101	896	95	below_threshold
Prosthecochloris vibrioformis	strain=DSM 260	GCA_006265245.1	1098	1098	type	True	77.4523	68	896	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	77.2652	63	896	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:16,978] [INFO] DFAST Taxonomy check result was written to GCF_003182595.1_ASM318259v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:16,979] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:16,979] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:16,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53dd48c7-58e3-4525-b8d4-1f8596bffb23/dqc_reference/checkm_data
[2024-01-24 13:02:16,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:17,010] [INFO] Task started: CheckM
[2024-01-24 13:02:17,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003182595.1_ASM318259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003182595.1_ASM318259v1_genomic.fna/checkm_input GCF_003182595.1_ASM318259v1_genomic.fna/checkm_result
[2024-01-24 13:03:02,695] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:02,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:02,719] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:02,719] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:02,720] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003182595.1_ASM318259v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:02,720] [INFO] Task started: Blastn
[2024-01-24 13:03:02,720] [INFO] Running command: blastn -query GCF_003182595.1_ASM318259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53dd48c7-58e3-4525-b8d4-1f8596bffb23/dqc_reference/reference_markers_gtdb.fasta -out GCF_003182595.1_ASM318259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:03,559] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:03,563] [INFO] Selected 14 target genomes.
[2024-01-24 13:03:03,564] [INFO] Target genome list was writen to GCF_003182595.1_ASM318259v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:03,629] [INFO] Task started: fastANI
[2024-01-24 13:03:03,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fd24a1a-8210-4f96-87d9-5f9808559a44/GCF_003182595.1_ASM318259v1_genomic.fna.gz --refList GCF_003182595.1_ASM318259v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003182595.1_ASM318259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:10,337] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:10,348] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:10,348] [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_003182595.1	s__Chlorobium_A marina	100.0	895	896	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium_A	95.0	98.89	98.89	0.95	0.95	2	conclusive
GCA_015482705.2	s__Chlorobium_A sp015482705	90.1984	769	896	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004028745.1	s__Chlorobium_A sp004028745	79.3474	331	896	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020545.1	s__Chlorobium_A phaeobacteroides_A	78.1724	234	896	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium_A	95.0	98.71	97.54	0.97	0.95	3	-
GCF_000020625.1	s__Prosthecochloris aestuarii	77.6256	101	896	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Prosthecochloris	95.0	98.26	98.17	0.90	0.89	3	-
GCF_002113825.1	s__Prosthecochloris sp002113825	77.0524	109	896	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Prosthecochloris	95.0	99.16	99.15	0.96	0.94	3	-
GCA_005862285.1	s__Chlorobium sp005862285	76.4017	52	896	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:10,350] [INFO] GTDB search result was written to GCF_003182595.1_ASM318259v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:10,351] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:10,363] [INFO] DFAST_QC result json was written to GCF_003182595.1_ASM318259v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:10,363] [INFO] DFAST_QC completed!
[2024-01-24 13:03:10,363] [INFO] Total running time: 0h1m20s