[2024-01-24 13:57:55,580] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:55,582] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:55,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg83735680-c1a7-4005-9baf-962abd3df61a/dqc_reference
[2024-01-24 13:57:56,987] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:56,988] [INFO] Task started: Prodigal
[2024-01-24 13:57:56,988] [INFO] Running command: gunzip -c /var/lib/cwl/stgf53a37a8-59f9-4373-8bb2-0f2086ebd13f/GCF_014191545.1_ASM1419154v1_genomic.fna.gz | prodigal -d GCF_014191545.1_ASM1419154v1_genomic.fna/cds.fna -a GCF_014191545.1_ASM1419154v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:06,180] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:06,180] [INFO] Task started: HMMsearch
[2024-01-24 13:58:06,180] [INFO] Running command: hmmsearch --tblout GCF_014191545.1_ASM1419154v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83735680-c1a7-4005-9baf-962abd3df61a/dqc_reference/reference_markers.hmm GCF_014191545.1_ASM1419154v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:06,496] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:06,503] [INFO] Found 6/6 markers.
[2024-01-24 13:58:06,532] [INFO] Query marker FASTA was written to GCF_014191545.1_ASM1419154v1_genomic.fna/markers.fasta
[2024-01-24 13:58:06,533] [INFO] Task started: Blastn
[2024-01-24 13:58:06,533] [INFO] Running command: blastn -query GCF_014191545.1_ASM1419154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83735680-c1a7-4005-9baf-962abd3df61a/dqc_reference/reference_markers.fasta -out GCF_014191545.1_ASM1419154v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:07,628] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:07,632] [INFO] Selected 30 target genomes.
[2024-01-24 13:58:07,633] [INFO] Target genome list was writen to GCF_014191545.1_ASM1419154v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:07,660] [INFO] Task started: fastANI
[2024-01-24 13:58:07,661] [INFO] Running command: fastANI --query /var/lib/cwl/stgf53a37a8-59f9-4373-8bb2-0f2086ebd13f/GCF_014191545.1_ASM1419154v1_genomic.fna.gz --refList GCF_014191545.1_ASM1419154v1_genomic.fna/target_genomes.txt --output GCF_014191545.1_ASM1419154v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:36,138] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:36,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83735680-c1a7-4005-9baf-962abd3df61a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:36,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83735680-c1a7-4005-9baf-962abd3df61a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:36,167] [INFO] Found 30 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:36,167] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:36,168] [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
Terrihabitans soli	strain=IZ6	GCA_014191545.1	708113	708113	type	True	100.0	1038	1038	95	conclusive
Microvirga ossetica	strain=V5/3M	GCA_002741015.1	1882682	1882682	type	True	77.7757	189	1038	95	below_threshold
Afipia carboxidovorans	strain=OM5; ATCC 49405	GCA_000021365.1	40137	40137	type	True	77.559	186	1038	95	below_threshold
Afipia carboxidovorans	strain=OM5	GCA_000218565.1	40137	40137	type	True	77.5413	187	1038	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	77.516	197	1038	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	77.5143	265	1038	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	77.4957	203	1038	95	below_threshold
Microvirga lotononidis	strain=WSM3557	GCA_000262405.1	864069	864069	type	True	77.4674	174	1038	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	77.4464	246	1038	95	below_threshold
Hansschlegelia beijingensis	strain=DSM 25481	GCA_014196425.1	1133344	1133344	type	True	77.366	217	1038	95	below_threshold
Agaricicola taiwanensis	strain=CCM 7684	GCA_014635245.1	591372	591372	type	True	77.3599	189	1038	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	77.3402	161	1038	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	77.3157	186	1038	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	77.2928	252	1038	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	77.2881	179	1038	95	below_threshold
Bradyrhizobium frederickii	strain=CNPSo 3426	GCA_004570865.1	2560054	2560054	type	True	77.255	238	1038	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	77.2485	191	1038	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	77.2111	179	1038	95	below_threshold
Bradyrhizobium zhanjiangense	strain=CCBAU 51778	GCA_004114935.1	1325107	1325107	type	True	77.19	242	1038	95	below_threshold
Azorhizobium doebereinerae	strain=UFLA1-100	GCA_000473085.1	281091	281091	type	True	77.1711	193	1038	95	below_threshold
Microvirga flocculans	strain=ATCC BAA-817	GCA_000518665.1	217168	217168	type	True	77.1641	156	1038	95	below_threshold
Pannonibacter carbonis	strain=Q4.6	GCA_003012935.1	2067569	2067569	type	True	77.1411	126	1038	95	below_threshold
Methylobacterium iners	strain=DSM 19015	GCA_022179305.1	418707	418707	type	True	77.1367	186	1038	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.1221	208	1038	95	below_threshold
Alsobacter soli	strain=SH9	GCA_003004785.1	2109933	2109933	type	True	77.0804	167	1038	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	77.0638	202	1038	95	below_threshold
Bradyrhizobium icense	strain=LMTR 13	GCA_001693385.1	1274631	1274631	type	True	77.025	219	1038	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	77.018	164	1038	95	below_threshold
Methylobacterium oxalidis	strain=NBRC 107715	GCA_007992195.1	944322	944322	type	True	76.8806	170	1038	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.8214	228	1038	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:36,169] [INFO] DFAST Taxonomy check result was written to GCF_014191545.1_ASM1419154v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:36,170] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:36,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:36,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83735680-c1a7-4005-9baf-962abd3df61a/dqc_reference/checkm_data
[2024-01-24 13:58:36,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:36,204] [INFO] Task started: CheckM
[2024-01-24 13:58:36,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191545.1_ASM1419154v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191545.1_ASM1419154v1_genomic.fna/checkm_input GCF_014191545.1_ASM1419154v1_genomic.fna/checkm_result
[2024-01-24 13:59:08,639] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:08,640] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:08,662] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:08,662] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:08,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191545.1_ASM1419154v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:08,663] [INFO] Task started: Blastn
[2024-01-24 13:59:08,663] [INFO] Running command: blastn -query GCF_014191545.1_ASM1419154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83735680-c1a7-4005-9baf-962abd3df61a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191545.1_ASM1419154v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:10,652] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:10,657] [INFO] Selected 19 target genomes.
[2024-01-24 13:59:10,657] [INFO] Target genome list was writen to GCF_014191545.1_ASM1419154v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:10,685] [INFO] Task started: fastANI
[2024-01-24 13:59:10,685] [INFO] Running command: fastANI --query /var/lib/cwl/stgf53a37a8-59f9-4373-8bb2-0f2086ebd13f/GCF_014191545.1_ASM1419154v1_genomic.fna.gz --refList GCF_014191545.1_ASM1419154v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191545.1_ASM1419154v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:26,258] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:26,278] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:26,279] [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
GCA_014191545.1	s__Ga0077545 sp014191545	100.0	1038	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Ga0077545	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001464335.1	s__Ga0077545 sp001464335	80.234	511	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Ga0077545	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003347645.1	s__Ga0077545 sp003347645	79.452	509	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Ga0077545	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745475.1	s__Bosea vestrisii	77.5499	245	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	98.16	98.02	0.92	0.87	6	-
GCF_003966715.1	s__Blastochloris tepida	77.4791	198	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142985.1	s__Bradyrhizobium erythrophlei_B	77.4007	199	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099825.1	s__Bradyrhizobium ottawaense_A	77.3892	217	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.73	99.45	0.98	0.96	3	-
GCF_014635245.1	s__Agaricicola taiwanensis	77.3599	189	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Agaricicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466745.1	s__Bosea sp900466745	77.3113	254	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.99	99.98	0.99	0.99	7	-
GCF_004103825.1	s__Hansschlegelia zhihuaiae	77.304	249	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001562255.1	s__Bosea sp001562255	77.2774	216	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899285.1	s__Pseudolabrys sp001899285	77.273	215	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	99.99	99.99	1.00	1.00	2	-
GCA_001898115.1	s__Bosea sp001898115	77.2697	226	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.21	98.43	0.96	0.93	3	-
GCA_001899525.1	s__65-9 sp001899525	77.151	185	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__65-9	95.0	99.88	99.88	0.96	0.96	2	-
GCF_001426225.1	s__Bosea sp001426225	77.1313	237	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519335.1	s__Jiella endophytica	77.0341	203	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001624695.1	s__Roseibium sp001624695	76.9435	103	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304555.1	s__JAFKKS01 sp017304555	76.8709	159	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__JAFKKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140315.1	s__PALSA-894 sp003140315	76.4475	185	1038	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__PALSA-894	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:26,281] [INFO] GTDB search result was written to GCF_014191545.1_ASM1419154v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:26,282] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:26,287] [INFO] DFAST_QC result json was written to GCF_014191545.1_ASM1419154v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:26,287] [INFO] DFAST_QC completed!
[2024-01-24 13:59:26,287] [INFO] Total running time: 0h1m31s