[2024-01-24 13:54:04,262] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:54:04,264] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:54:04,264] [INFO] DQC Reference Directory: /var/lib/cwl/stge77d3bbe-9d42-4129-8c6d-4a41556e5664/dqc_reference
[2024-01-24 13:54:05,692] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:54:05,693] [INFO] Task started: Prodigal
[2024-01-24 13:54:05,693] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1a0c264-82c0-4e7b-899c-09475999399b/GCF_008312935.1_ASM831293v1_genomic.fna.gz | prodigal -d GCF_008312935.1_ASM831293v1_genomic.fna/cds.fna -a GCF_008312935.1_ASM831293v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:54:34,933] [INFO] Task succeeded: Prodigal
[2024-01-24 13:54:34,934] [INFO] Task started: HMMsearch
[2024-01-24 13:54:34,934] [INFO] Running command: hmmsearch --tblout GCF_008312935.1_ASM831293v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge77d3bbe-9d42-4129-8c6d-4a41556e5664/dqc_reference/reference_markers.hmm GCF_008312935.1_ASM831293v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:54:35,326] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:54:35,327] [INFO] Found 6/6 markers.
[2024-01-24 13:54:35,388] [INFO] Query marker FASTA was written to GCF_008312935.1_ASM831293v1_genomic.fna/markers.fasta
[2024-01-24 13:54:35,388] [INFO] Task started: Blastn
[2024-01-24 13:54:35,389] [INFO] Running command: blastn -query GCF_008312935.1_ASM831293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge77d3bbe-9d42-4129-8c6d-4a41556e5664/dqc_reference/reference_markers.fasta -out GCF_008312935.1_ASM831293v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:54:36,020] [INFO] Task succeeded: Blastn
[2024-01-24 13:54:36,023] [INFO] Selected 17 target genomes.
[2024-01-24 13:54:36,023] [INFO] Target genome list was writen to GCF_008312935.1_ASM831293v1_genomic.fna/target_genomes.txt
[2024-01-24 13:54:36,055] [INFO] Task started: fastANI
[2024-01-24 13:54:36,055] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1a0c264-82c0-4e7b-899c-09475999399b/GCF_008312935.1_ASM831293v1_genomic.fna.gz --refList GCF_008312935.1_ASM831293v1_genomic.fna/target_genomes.txt --output GCF_008312935.1_ASM831293v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:54:59,883] [INFO] Task succeeded: fastANI
[2024-01-24 13:54:59,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge77d3bbe-9d42-4129-8c6d-4a41556e5664/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:54:59,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge77d3bbe-9d42-4129-8c6d-4a41556e5664/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:54:59,895] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:54:59,895] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:54:59,895] [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
Roseiconus lacunae	strain=JC635	GCA_008312935.1	2605694	2605694	type	True	100.0	2603	2609	95	conclusive
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	78.0633	377	2609	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	77.2787	164	2609	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	77.1917	396	2609	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	76.9712	282	2609	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	76.8825	208	2609	95	below_threshold
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	76.6304	118	2609	95	below_threshold
Rubripirellula tenax	strain=Poly51	GCA_007860125.1	2528015	2528015	type	True	76.4681	142	2609	95	below_threshold
Roseimaritima ulvae	strain=DSM 25454	GCA_001642915.1	980254	980254	type	True	76.4336	126	2609	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	76.4283	143	2609	95	below_threshold
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	76.2616	157	2609	95	below_threshold
Novipirellula galeiformis	strain=Pla52o	GCA_007860095.1	2528004	2528004	type	True	76.1904	115	2609	95	below_threshold
Rhodopirellula maiorica	strain=SM1	GCA_000346295.1	1265734	1265734	type	True	76.081	140	2609	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:54:59,896] [INFO] DFAST Taxonomy check result was written to GCF_008312935.1_ASM831293v1_genomic.fna/tc_result.tsv
[2024-01-24 13:54:59,897] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:54:59,897] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:54:59,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge77d3bbe-9d42-4129-8c6d-4a41556e5664/dqc_reference/checkm_data
[2024-01-24 13:54:59,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:54:59,976] [INFO] Task started: CheckM
[2024-01-24 13:54:59,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008312935.1_ASM831293v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008312935.1_ASM831293v1_genomic.fna/checkm_input GCF_008312935.1_ASM831293v1_genomic.fna/checkm_result
[2024-01-24 13:56:17,172] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:17,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:17,200] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:17,200] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:17,201] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008312935.1_ASM831293v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:17,201] [INFO] Task started: Blastn
[2024-01-24 13:56:17,201] [INFO] Running command: blastn -query GCF_008312935.1_ASM831293v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge77d3bbe-9d42-4129-8c6d-4a41556e5664/dqc_reference/reference_markers_gtdb.fasta -out GCF_008312935.1_ASM831293v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:18,040] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:18,045] [INFO] Selected 11 target genomes.
[2024-01-24 13:56:18,045] [INFO] Target genome list was writen to GCF_008312935.1_ASM831293v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:18,078] [INFO] Task started: fastANI
[2024-01-24 13:56:18,079] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1a0c264-82c0-4e7b-899c-09475999399b/GCF_008312935.1_ASM831293v1_genomic.fna.gz --refList GCF_008312935.1_ASM831293v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008312935.1_ASM831293v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:35,263] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:35,272] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:35,273] [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_008312935.1	s__Stieleria lacunae	100.0	2603	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002901265.1	s__Stieleria baltica_A	78.5991	679	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.97	99.97	0.98	0.98	2	-
GCF_008035925.1	s__Stieleria maiorica	78.0447	379	2609	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	77.7108	399	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014154935.1	s__Stieleria sp014154935	77.6917	380	2609	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	77.1956	394	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629675.1	s__Stieleria nitratireducens	76.971	282	2609	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	76.8734	383	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860125.1	s__Rubripirellula tenax	76.427	145	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346295.1	s__Novipirellula maiorica	76.136	140	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002428205.1	s__UBA6163 sp002428205	75.2183	59	2609	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA6163	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:35,274] [INFO] GTDB search result was written to GCF_008312935.1_ASM831293v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:35,275] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:35,278] [INFO] DFAST_QC result json was written to GCF_008312935.1_ASM831293v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:35,278] [INFO] DFAST_QC completed!
[2024-01-24 13:56:35,278] [INFO] Total running time: 0h2m31s