[2024-01-24 13:48:59,896] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,897] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,897] [INFO] DQC Reference Directory: /var/lib/cwl/stg502bc987-ab2f-46c9-9b50-fb1f1d659b41/dqc_reference
[2024-01-24 13:49:01,193] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,194] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,194] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4144b47-fa27-482e-ab83-01fee52625eb/GCF_000022145.1_ASM2214v1_genomic.fna.gz | prodigal -d GCF_000022145.1_ASM2214v1_genomic.fna/cds.fna -a GCF_000022145.1_ASM2214v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:14,386] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:14,386] [INFO] Task started: HMMsearch
[2024-01-24 13:49:14,387] [INFO] Running command: hmmsearch --tblout GCF_000022145.1_ASM2214v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg502bc987-ab2f-46c9-9b50-fb1f1d659b41/dqc_reference/reference_markers.hmm GCF_000022145.1_ASM2214v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:14,677] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:14,678] [INFO] Found 6/6 markers.
[2024-01-24 13:49:14,718] [INFO] Query marker FASTA was written to GCF_000022145.1_ASM2214v1_genomic.fna/markers.fasta
[2024-01-24 13:49:14,718] [INFO] Task started: Blastn
[2024-01-24 13:49:14,718] [INFO] Running command: blastn -query GCF_000022145.1_ASM2214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg502bc987-ab2f-46c9-9b50-fb1f1d659b41/dqc_reference/reference_markers.fasta -out GCF_000022145.1_ASM2214v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:15,556] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:15,559] [INFO] Selected 29 target genomes.
[2024-01-24 13:49:15,559] [INFO] Target genome list was writen to GCF_000022145.1_ASM2214v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:15,569] [INFO] Task started: fastANI
[2024-01-24 13:49:15,569] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4144b47-fa27-482e-ab83-01fee52625eb/GCF_000022145.1_ASM2214v1_genomic.fna.gz --refList GCF_000022145.1_ASM2214v1_genomic.fna/target_genomes.txt --output GCF_000022145.1_ASM2214v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:58,662] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:58,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg502bc987-ab2f-46c9-9b50-fb1f1d659b41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:58,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg502bc987-ab2f-46c9-9b50-fb1f1d659b41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:58,688] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:58,688] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:58,688] [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
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	100.0	1675	1676	95	conclusive
Stigmatella aurantiaca	strain=DSM 17044	GCA_900109545.1	41	41	type	True	76.1874	439	1676	95	below_threshold
Stigmatella hybrida	strain=DSM 14722	GCA_020103775.1	394097	394097	type	True	76.1736	432	1676	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	76.1523	452	1676	95	below_threshold
Corallococcus sicarius	strain=CA040B	GCA_003611735.1	2316726	2316726	type	True	76.0986	485	1676	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	76.0846	546	1676	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	76.0481	423	1676	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	76.0144	551	1676	95	below_threshold
Myxococcus eversor	strain=AB053B	GCA_010894455.1	2709661	2709661	type	True	75.9825	454	1676	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	75.9444	419	1676	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	75.9386	541	1676	95	below_threshold
Pyxidicoccus fallax	strain=DSM 14698	GCA_012933655.1	394095	394095	type	True	75.8354	589	1676	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	75.7755	556	1676	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	75.7644	603	1676	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	75.6533	136	1676	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	75.5366	133	1676	95	below_threshold
Lysobacter luteus	strain=CECT 30171	GCA_907164845.1	2822368	2822368	type	True	75.4674	142	1676	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	75.3602	195	1676	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.3139	210	1676	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_900101365.1	381306	381306	type	True	75.3118	141	1676	95	below_threshold
Chromohalobacter salexigens	strain=DSM 3043	GCA_000055785.1	158080	158080	type	True	75.1857	85	1676	95	below_threshold
Crenobacter sedimenti	strain=HX-7-9	GCA_010435965.1	2705474	2705474	type	True	75.1524	191	1676	95	below_threshold
Thauera phenylacetica	strain=B4P	GCA_000310225.1	164400	164400	type	True	75.1351	311	1676	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	75.1139	235	1676	95	below_threshold
Lujinxingia vulgaris	strain=TMQ4	GCA_007997015.1	2600176	2600176	type	True	75.0359	117	1676	95	below_threshold
Cohnella nanjingensis	strain=DSM 28246	GCA_014212125.1	1387779	1387779	type	True	75.0127	93	1676	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	74.873	380	1676	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	74.8197	68	1676	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:58,690] [INFO] DFAST Taxonomy check result was written to GCF_000022145.1_ASM2214v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:58,691] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:58,691] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:58,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg502bc987-ab2f-46c9-9b50-fb1f1d659b41/dqc_reference/checkm_data
[2024-01-24 13:49:58,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:58,744] [INFO] Task started: CheckM
[2024-01-24 13:49:58,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000022145.1_ASM2214v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000022145.1_ASM2214v1_genomic.fna/checkm_input GCF_000022145.1_ASM2214v1_genomic.fna/checkm_result
[2024-01-24 13:51:10,238] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:10,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:10,260] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:10,261] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:10,261] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000022145.1_ASM2214v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:10,262] [INFO] Task started: Blastn
[2024-01-24 13:51:10,262] [INFO] Running command: blastn -query GCF_000022145.1_ASM2214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg502bc987-ab2f-46c9-9b50-fb1f1d659b41/dqc_reference/reference_markers_gtdb.fasta -out GCF_000022145.1_ASM2214v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:11,661] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:11,664] [INFO] Selected 7 target genomes.
[2024-01-24 13:51:11,665] [INFO] Target genome list was writen to GCF_000022145.1_ASM2214v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:11,678] [INFO] Task started: fastANI
[2024-01-24 13:51:11,678] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4144b47-fa27-482e-ab83-01fee52625eb/GCF_000022145.1_ASM2214v1_genomic.fna.gz --refList GCF_000022145.1_ASM2214v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000022145.1_ASM2214v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:24,777] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:24,790] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:24,790] [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_000022145.1	s__Anaeromyxobacter dehalogenans	100.0	1675	1676	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	97.16	97.16	0.92	0.92	2	conclusive
GCF_000013385.1	s__Anaeromyxobacter dehalogenans_B	93.8956	1506	1676	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964525.1	s__Anaeromyxobacter sp000964525	93.3831	1251	1676	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017505.1	s__Anaeromyxobacter sp000017505	81.2316	1023	1676	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013340205.1	s__R267 sp013340205	79.9654	933	1676	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__R267	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016718565.1	s__JADKCZ01 sp016718565	79.6966	881	1676	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__JADKCZ01	95.0	99.81	99.81	0.97	0.97	2	-
GCA_903874275.1	s__CAIOAK01 sp903874275	78.9041	599	1676	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__CAIOAK01	95.0	99.83	99.81	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:24,792] [INFO] GTDB search result was written to GCF_000022145.1_ASM2214v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:24,793] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:24,800] [INFO] DFAST_QC result json was written to GCF_000022145.1_ASM2214v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:24,800] [INFO] DFAST_QC completed!
[2024-01-24 13:51:24,800] [INFO] Total running time: 0h2m25s