[2024-01-24 13:41:10,389] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,391] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,391] [INFO] DQC Reference Directory: /var/lib/cwl/stgc08865ab-1b6d-4c11-8f68-69d0cbcf6a09/dqc_reference
[2024-01-24 13:41:11,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:11,723] [INFO] Task started: Prodigal
[2024-01-24 13:41:11,723] [INFO] Running command: gunzip -c /var/lib/cwl/stga7599172-3541-4d3a-8218-c97de156dfcb/GCF_000315035.1_ASM31503v1_genomic.fna.gz | prodigal -d GCF_000315035.1_ASM31503v1_genomic.fna/cds.fna -a GCF_000315035.1_ASM31503v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:21,742] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:21,743] [INFO] Task started: HMMsearch
[2024-01-24 13:41:21,743] [INFO] Running command: hmmsearch --tblout GCF_000315035.1_ASM31503v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc08865ab-1b6d-4c11-8f68-69d0cbcf6a09/dqc_reference/reference_markers.hmm GCF_000315035.1_ASM31503v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:22,095] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:22,096] [INFO] Found 6/6 markers.
[2024-01-24 13:41:22,135] [INFO] Query marker FASTA was written to GCF_000315035.1_ASM31503v1_genomic.fna/markers.fasta
[2024-01-24 13:41:22,135] [INFO] Task started: Blastn
[2024-01-24 13:41:22,135] [INFO] Running command: blastn -query GCF_000315035.1_ASM31503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc08865ab-1b6d-4c11-8f68-69d0cbcf6a09/dqc_reference/reference_markers.fasta -out GCF_000315035.1_ASM31503v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:22,887] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:22,890] [INFO] Selected 20 target genomes.
[2024-01-24 13:41:22,891] [INFO] Target genome list was writen to GCF_000315035.1_ASM31503v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:22,904] [INFO] Task started: fastANI
[2024-01-24 13:41:22,905] [INFO] Running command: fastANI --query /var/lib/cwl/stga7599172-3541-4d3a-8218-c97de156dfcb/GCF_000315035.1_ASM31503v1_genomic.fna.gz --refList GCF_000315035.1_ASM31503v1_genomic.fna/target_genomes.txt --output GCF_000315035.1_ASM31503v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:38,047] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:38,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc08865ab-1b6d-4c11-8f68-69d0cbcf6a09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:38,048] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc08865ab-1b6d-4c11-8f68-69d0cbcf6a09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:38,058] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:38,058] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:38,059] [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
Glaciecola pallidula	strain=ACAM 615	GCA_000315035.1	56807	56807	type	True	100.0	1415	1418	95	conclusive
Glaciecola pallidula	strain=DSM 14239	GCA_000428905.1	56807	56807	type	True	99.9956	1410	1418	95	conclusive
Glaciecola nitratireducens	strain=FR1064	GCA_000226565.1	300231	300231	type	True	79.8027	603	1418	95	below_threshold
Glaciecola punicea	strain=ACAM 611	GCA_000252165.2	56804	56804	type	True	79.2643	123	1418	95	below_threshold
Ningiella ruwaisensis	strain=B66	GCA_004798935.1	2364274	2364274	type	True	78.0699	66	1418	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	77.6572	61	1418	95	below_threshold
Paraglaciecola mesophila	strain=KMM 241	GCA_000315015.1	197222	197222	type	True	77.6492	65	1418	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	77.4838	64	1418	95	below_threshold
Aliiglaciecola lipolytica	strain=E3	GCA_000314975.1	477689	477689	type	True	77.3992	60	1418	95	below_threshold
Paraglaciecola marina	strain=D3211	GCA_004360155.1	2500157	2500157	type	True	77.3796	69	1418	95	below_threshold
Alteromonas sediminis	strain=U0105	GCA_003820355.1	2259342	2259342	type	True	77.261	51	1418	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	77.104	72	1418	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:38,060] [INFO] DFAST Taxonomy check result was written to GCF_000315035.1_ASM31503v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:38,061] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:38,061] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:38,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc08865ab-1b6d-4c11-8f68-69d0cbcf6a09/dqc_reference/checkm_data
[2024-01-24 13:41:38,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:38,110] [INFO] Task started: CheckM
[2024-01-24 13:41:38,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000315035.1_ASM31503v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000315035.1_ASM31503v1_genomic.fna/checkm_input GCF_000315035.1_ASM31503v1_genomic.fna/checkm_result
[2024-01-24 13:42:12,593] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:12,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:12,617] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:12,618] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:12,618] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000315035.1_ASM31503v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:12,618] [INFO] Task started: Blastn
[2024-01-24 13:42:12,619] [INFO] Running command: blastn -query GCF_000315035.1_ASM31503v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc08865ab-1b6d-4c11-8f68-69d0cbcf6a09/dqc_reference/reference_markers_gtdb.fasta -out GCF_000315035.1_ASM31503v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:13,695] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:13,699] [INFO] Selected 14 target genomes.
[2024-01-24 13:42:13,699] [INFO] Target genome list was writen to GCF_000315035.1_ASM31503v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:13,716] [INFO] Task started: fastANI
[2024-01-24 13:42:13,716] [INFO] Running command: fastANI --query /var/lib/cwl/stga7599172-3541-4d3a-8218-c97de156dfcb/GCF_000315035.1_ASM31503v1_genomic.fna.gz --refList GCF_000315035.1_ASM31503v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000315035.1_ASM31503v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:24,008] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:24,027] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:24,027] [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_000428905.1	s__Glaciecola pallidula	99.9956	1410	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_002836745.1	s__Glaciecola sp002836745	91.9377	1155	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000226565.1	s__Glaciecola nitratireducens	79.794	604	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000252165.1	s__Glaciecola punicea	79.2929	124	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	99.53	99.53	0.94	0.94	2	-
GCA_905479945.1	s__Glaciecola sp905479945	78.5443	369	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003203515.1	s__Glaciecola sp003203515	77.909	112	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015595035.1	s__Glaciecola sp015595035	77.8993	196	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172635.2	s__Alteromonas macleodii	77.6466	63	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_009796745.1	s__Paraglaciecola sp009796745	77.5885	73	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903772925.1	s__Alteromonas macleodii_A	77.3858	64	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003820355.1	s__Alteromonas_F sediminis	77.2841	52	1418	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:24,029] [INFO] GTDB search result was written to GCF_000315035.1_ASM31503v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:24,030] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:24,034] [INFO] DFAST_QC result json was written to GCF_000315035.1_ASM31503v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:24,034] [INFO] DFAST_QC completed!
[2024-01-24 13:42:24,034] [INFO] Total running time: 0h1m14s