[2024-01-25 18:03:05,896] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:05,901] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:05,901] [INFO] DQC Reference Directory: /var/lib/cwl/stg101c08d9-725a-4de9-9e25-f9ce6ef63db0/dqc_reference
[2024-01-25 18:03:07,129] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:07,130] [INFO] Task started: Prodigal
[2024-01-25 18:03:07,130] [INFO] Running command: gunzip -c /var/lib/cwl/stg45f9888f-4927-468e-a4b0-93097729cfdf/GCF_014192335.1_ASM1419233v1_genomic.fna.gz | prodigal -d GCF_014192335.1_ASM1419233v1_genomic.fna/cds.fna -a GCF_014192335.1_ASM1419233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:34,729] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:34,730] [INFO] Task started: HMMsearch
[2024-01-25 18:03:34,730] [INFO] Running command: hmmsearch --tblout GCF_014192335.1_ASM1419233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg101c08d9-725a-4de9-9e25-f9ce6ef63db0/dqc_reference/reference_markers.hmm GCF_014192335.1_ASM1419233v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:35,145] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:35,146] [INFO] Found 6/6 markers.
[2024-01-25 18:03:35,210] [INFO] Query marker FASTA was written to GCF_014192335.1_ASM1419233v1_genomic.fna/markers.fasta
[2024-01-25 18:03:35,210] [INFO] Task started: Blastn
[2024-01-25 18:03:35,210] [INFO] Running command: blastn -query GCF_014192335.1_ASM1419233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg101c08d9-725a-4de9-9e25-f9ce6ef63db0/dqc_reference/reference_markers.fasta -out GCF_014192335.1_ASM1419233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:35,792] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:35,796] [INFO] Selected 14 target genomes.
[2024-01-25 18:03:35,797] [INFO] Target genome list was writen to GCF_014192335.1_ASM1419233v1_genomic.fna/target_genomes.txt
[2024-01-25 18:03:35,815] [INFO] Task started: fastANI
[2024-01-25 18:03:35,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg45f9888f-4927-468e-a4b0-93097729cfdf/GCF_014192335.1_ASM1419233v1_genomic.fna.gz --refList GCF_014192335.1_ASM1419233v1_genomic.fna/target_genomes.txt --output GCF_014192335.1_ASM1419233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:54,817] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:54,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg101c08d9-725a-4de9-9e25-f9ce6ef63db0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:54,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg101c08d9-725a-4de9-9e25-f9ce6ef63db0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:54,828] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:54,828] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:54,828] [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
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	100.0	2811	2812	95	conclusive
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	80.8208	1332	2812	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	79.8701	1111	2812	95	below_threshold
Rubripirellula obstinata	strain=CECT 8602	GCA_001642955.1	406547	406547	type	True	78.2203	220	2812	95	below_threshold
Rhodopirellula baltica	strain=1	GCA_000196115.1	265606	265606	type	True	77.9647	303	2812	95	below_threshold
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	77.8437	421	2812	95	below_threshold
Rhodopirellula solitaria	strain=CA85	GCA_007859855.1	2527987	2527987	type	True	77.2751	395	2812	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	77.1959	281	2812	95	below_threshold
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	77.1952	290	2812	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	76.6652	159	2812	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:54,830] [INFO] DFAST Taxonomy check result was written to GCF_014192335.1_ASM1419233v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:54,830] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:54,830] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:54,830] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg101c08d9-725a-4de9-9e25-f9ce6ef63db0/dqc_reference/checkm_data
[2024-01-25 18:03:54,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:54,913] [INFO] Task started: CheckM
[2024-01-25 18:03:54,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014192335.1_ASM1419233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014192335.1_ASM1419233v1_genomic.fna/checkm_input GCF_014192335.1_ASM1419233v1_genomic.fna/checkm_result
[2024-01-25 18:05:15,103] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:15,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:15,122] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:15,123] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:15,124] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014192335.1_ASM1419233v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:15,124] [INFO] Task started: Blastn
[2024-01-25 18:05:15,124] [INFO] Running command: blastn -query GCF_014192335.1_ASM1419233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg101c08d9-725a-4de9-9e25-f9ce6ef63db0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014192335.1_ASM1419233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:15,939] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:15,942] [INFO] Selected 14 target genomes.
[2024-01-25 18:05:15,942] [INFO] Target genome list was writen to GCF_014192335.1_ASM1419233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:15,950] [INFO] Task started: fastANI
[2024-01-25 18:05:15,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg45f9888f-4927-468e-a4b0-93097729cfdf/GCF_014192335.1_ASM1419233v1_genomic.fna.gz --refList GCF_014192335.1_ASM1419233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014192335.1_ASM1419233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:34,288] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:34,296] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:34,297] [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_014192335.1	s__Rhodopirellula rubra	100.0	2811	2812	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	95.37	95.37	0.86	0.86	2	conclusive
GCF_000346505.1	s__Rhodopirellula sallentina	79.8623	1113	2812	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007859835.1	s__Novipirellula sp007859835	78.7095	178	2812	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642955.1	s__Rubripirellula obstinata	78.215	221	2812	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	99.93	99.93	1.00	1.00	2	-
GCF_000196115.1	s__Rhodopirellula baltica	77.9677	304	2812	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	97.96	97.13	0.94	0.89	5	-
GCF_007859915.1	s__Rhodopirellula pilleata	77.813	425	2812	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007860105.1	s__Rhodopirellula sp007860105	77.7934	358	2812	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002727185.1	s__Rhodopirellula bahusiensis	77.433	321	2812	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859855.1	s__Rhodopirellula solitaria	77.2751	395	2812	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027925.1	s__Rhodopirellula islandica	77.2151	279	2812	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338295.1	s__Rhodopirellula europaea	77.205	289	2812	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	-
GCF_008629675.1	s__Stieleria nitratireducens	76.6652	159	2812	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860095.1	s__Novipirellula galeiformis	76.647	151	2812	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:34,298] [INFO] GTDB search result was written to GCF_014192335.1_ASM1419233v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:34,298] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:34,301] [INFO] DFAST_QC result json was written to GCF_014192335.1_ASM1419233v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:34,301] [INFO] DFAST_QC completed!
[2024-01-25 18:05:34,301] [INFO] Total running time: 0h2m28s