[2024-01-24 12:06:14,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg9496061a-61fb-4974-bf6b-4941c971ef9d/dqc_reference
[2024-01-24 12:06:16,113] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:16,114] [INFO] Task started: Prodigal
[2024-01-24 12:06:16,114] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e3258f2-312c-4331-a4a1-c4f34e4e30e7/GCF_024129865.1_ASM2412986v1_genomic.fna.gz | prodigal -d GCF_024129865.1_ASM2412986v1_genomic.fna/cds.fna -a GCF_024129865.1_ASM2412986v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:51,219] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:51,220] [INFO] Task started: HMMsearch
[2024-01-24 12:06:51,220] [INFO] Running command: hmmsearch --tblout GCF_024129865.1_ASM2412986v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9496061a-61fb-4974-bf6b-4941c971ef9d/dqc_reference/reference_markers.hmm GCF_024129865.1_ASM2412986v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:51,654] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:51,655] [INFO] Found 6/6 markers.
[2024-01-24 12:06:51,723] [INFO] Query marker FASTA was written to GCF_024129865.1_ASM2412986v1_genomic.fna/markers.fasta
[2024-01-24 12:06:51,723] [INFO] Task started: Blastn
[2024-01-24 12:06:51,723] [INFO] Running command: blastn -query GCF_024129865.1_ASM2412986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9496061a-61fb-4974-bf6b-4941c971ef9d/dqc_reference/reference_markers.fasta -out GCF_024129865.1_ASM2412986v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:52,428] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:52,433] [INFO] Selected 17 target genomes.
[2024-01-24 12:06:52,434] [INFO] Target genome list was writen to GCF_024129865.1_ASM2412986v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:52,455] [INFO] Task started: fastANI
[2024-01-24 12:06:52,456] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e3258f2-312c-4331-a4a1-c4f34e4e30e7/GCF_024129865.1_ASM2412986v1_genomic.fna.gz --refList GCF_024129865.1_ASM2412986v1_genomic.fna/target_genomes.txt --output GCF_024129865.1_ASM2412986v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:13,832] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:13,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9496061a-61fb-4974-bf6b-4941c971ef9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:13,834] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9496061a-61fb-4974-bf6b-4941c971ef9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:13,847] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:13,847] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:13,847] [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
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	77.9494	646	2490	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	77.8259	255	2490	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	77.8151	651	2490	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	77.3394	242	2490	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	77.2748	432	2490	95	below_threshold
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	77.1526	177	2490	95	below_threshold
Roseiconus lacunae	strain=JC635	GCA_008312935.1	2605694	2605694	type	True	77.0745	297	2490	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	76.8781	271	2490	95	below_threshold
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	76.8757	198	2490	95	below_threshold
Rosistilla carotiformis	strain=Poly24	GCA_007753095.1	2528017	2528017	type	True	76.8712	142	2490	95	below_threshold
Rhodopirellula baltica	strain=1	GCA_000196115.1	265606	265606	type	True	76.7611	187	2490	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	75.9612	168	2490	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:13,849] [INFO] DFAST Taxonomy check result was written to GCF_024129865.1_ASM2412986v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:13,850] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:13,850] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:13,850] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9496061a-61fb-4974-bf6b-4941c971ef9d/dqc_reference/checkm_data
[2024-01-24 12:07:13,851] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:13,924] [INFO] Task started: CheckM
[2024-01-24 12:07:13,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024129865.1_ASM2412986v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024129865.1_ASM2412986v1_genomic.fna/checkm_input GCF_024129865.1_ASM2412986v1_genomic.fna/checkm_result
[2024-01-24 12:08:50,353] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:50,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:50,381] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:50,382] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:50,382] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024129865.1_ASM2412986v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:50,383] [INFO] Task started: Blastn
[2024-01-24 12:08:50,383] [INFO] Running command: blastn -query GCF_024129865.1_ASM2412986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9496061a-61fb-4974-bf6b-4941c971ef9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_024129865.1_ASM2412986v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:51,211] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:51,215] [INFO] Selected 17 target genomes.
[2024-01-24 12:08:51,215] [INFO] Target genome list was writen to GCF_024129865.1_ASM2412986v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:51,243] [INFO] Task started: fastANI
[2024-01-24 12:08:51,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e3258f2-312c-4331-a4a1-c4f34e4e30e7/GCF_024129865.1_ASM2412986v1_genomic.fna.gz --refList GCF_024129865.1_ASM2412986v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024129865.1_ASM2412986v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:10,150] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:10,164] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:09:10,164] [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_014154935.1	s__Stieleria sp014154935	78.1244	650	2490	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007753675.1	s__Stieleria sp007753675	78.0353	649	2490	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007754155.1	s__Stieleria neptunia	77.9601	644	2490	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008035925.1	s__Stieleria maiorica	77.8186	648	2490	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289565.1	s__Stieleria sp002289565	77.7814	592	2490	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007859835.1	s__Novipirellula sp007859835	77.2876	140	2490	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629675.1	s__Stieleria nitratireducens	77.268	433	2490	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312935.1	s__Stieleria lacunae	77.066	297	2490	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002901265.1	s__Stieleria baltica_A	77.0631	306	2490	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.97	99.97	0.98	0.98	2	-
GCF_007860045.1	s__Stieleria varia	76.8781	271	2490	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862205.1	s__Rubripirellula sp002862205	75.6022	74	2490	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:10,166] [INFO] GTDB search result was written to GCF_024129865.1_ASM2412986v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:10,167] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:10,170] [INFO] DFAST_QC result json was written to GCF_024129865.1_ASM2412986v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:10,171] [INFO] DFAST_QC completed!
[2024-01-24 12:09:10,171] [INFO] Total running time: 0h2m55s