[2023-06-30 03:29:07,673] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:29:07,678] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:29:07,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b21c445-a09d-47a0-84e6-b5059d9e7f97/dqc_reference
[2023-06-30 03:29:09,143] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:29:09,147] [INFO] Task started: Prodigal
[2023-06-30 03:29:09,148] [INFO] Running command: gunzip -c /var/lib/cwl/stg621ed86e-90fa-45fc-a2f9-969963d1406a/GCA_016708055.1_ASM1670805v1_genomic.fna.gz | prodigal -d GCA_016708055.1_ASM1670805v1_genomic.fna/cds.fna -a GCA_016708055.1_ASM1670805v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:29:19,942] [INFO] Task succeeded: Prodigal
[2023-06-30 03:29:19,942] [INFO] Task started: HMMsearch
[2023-06-30 03:29:19,942] [INFO] Running command: hmmsearch --tblout GCA_016708055.1_ASM1670805v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b21c445-a09d-47a0-84e6-b5059d9e7f97/dqc_reference/reference_markers.hmm GCA_016708055.1_ASM1670805v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:29:20,185] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:29:20,187] [INFO] Found 6/6 markers.
[2023-06-30 03:29:20,219] [INFO] Query marker FASTA was written to GCA_016708055.1_ASM1670805v1_genomic.fna/markers.fasta
[2023-06-30 03:29:20,220] [INFO] Task started: Blastn
[2023-06-30 03:29:20,220] [INFO] Running command: blastn -query GCA_016708055.1_ASM1670805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b21c445-a09d-47a0-84e6-b5059d9e7f97/dqc_reference/reference_markers.fasta -out GCA_016708055.1_ASM1670805v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:29:21,108] [INFO] Task succeeded: Blastn
[2023-06-30 03:29:21,112] [INFO] Selected 22 target genomes.
[2023-06-30 03:29:21,112] [INFO] Target genome list was writen to GCA_016708055.1_ASM1670805v1_genomic.fna/target_genomes.txt
[2023-06-30 03:29:21,113] [INFO] Task started: fastANI
[2023-06-30 03:29:21,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg621ed86e-90fa-45fc-a2f9-969963d1406a/GCA_016708055.1_ASM1670805v1_genomic.fna.gz --refList GCA_016708055.1_ASM1670805v1_genomic.fna/target_genomes.txt --output GCA_016708055.1_ASM1670805v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:29:40,634] [INFO] Task succeeded: fastANI
[2023-06-30 03:29:40,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b21c445-a09d-47a0-84e6-b5059d9e7f97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:29:40,635] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b21c445-a09d-47a0-84e6-b5059d9e7f97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:29:40,658] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:29:40,658] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:29:40,658] [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
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	77.7232	170	1095	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	77.6583	167	1095	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	77.4267	181	1095	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	77.3242	172	1095	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	77.2861	173	1095	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	76.9539	173	1095	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	76.9523	169	1095	95	below_threshold
Thiohalocapsa marina	strain=DSM 19078	GCA_008632335.1	424902	424902	type	True	76.8466	122	1095	95	below_threshold
Lysobacter aestuarii	strain=JCM 31130	GCA_006546775.1	1706195	1706195	type	True	76.787	136	1095	95	below_threshold
Sulfuritortus calidifontis	strain=J1A	GCA_003967275.1	1914471	1914471	type	True	76.7405	101	1095	95	below_threshold
Sulfuritortus calidifontis	strain=DSM 103923	GCA_004346085.1	1914471	1914471	type	True	76.7275	99	1095	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	76.6598	187	1095	95	below_threshold
Thiobacillus thioparus	strain=DSM 505	GCA_000373385.1	931	931	type	True	76.4933	91	1095	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.4427	204	1095	95	below_threshold
Fluviicoccus keumensis	strain=DSM 105135	GCA_004217445.1	1435465	1435465	type	True	76.3235	72	1095	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	76.1043	160	1095	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	76.0905	172	1095	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	76.0589	255	1095	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	76.0349	234	1095	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	76.022	260	1095	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	75.1311	119	1095	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:29:40,660] [INFO] DFAST Taxonomy check result was written to GCA_016708055.1_ASM1670805v1_genomic.fna/tc_result.tsv
[2023-06-30 03:29:40,661] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:29:40,661] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:29:40,661] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b21c445-a09d-47a0-84e6-b5059d9e7f97/dqc_reference/checkm_data
[2023-06-30 03:29:40,662] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:29:40,701] [INFO] Task started: CheckM
[2023-06-30 03:29:40,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708055.1_ASM1670805v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708055.1_ASM1670805v1_genomic.fna/checkm_input GCA_016708055.1_ASM1670805v1_genomic.fna/checkm_result
[2023-06-30 03:30:19,444] [INFO] Task succeeded: CheckM
[2023-06-30 03:30:19,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:30:19,468] [INFO] ===== Completeness check finished =====
[2023-06-30 03:30:19,468] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:30:19,469] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708055.1_ASM1670805v1_genomic.fna/markers.fasta)
[2023-06-30 03:30:19,469] [INFO] Task started: Blastn
[2023-06-30 03:30:19,469] [INFO] Running command: blastn -query GCA_016708055.1_ASM1670805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b21c445-a09d-47a0-84e6-b5059d9e7f97/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708055.1_ASM1670805v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:30:21,019] [INFO] Task succeeded: Blastn
[2023-06-30 03:30:21,026] [INFO] Selected 17 target genomes.
[2023-06-30 03:30:21,026] [INFO] Target genome list was writen to GCA_016708055.1_ASM1670805v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:30:21,030] [INFO] Task started: fastANI
[2023-06-30 03:30:21,030] [INFO] Running command: fastANI --query /var/lib/cwl/stg621ed86e-90fa-45fc-a2f9-969963d1406a/GCA_016708055.1_ASM1670805v1_genomic.fna.gz --refList GCA_016708055.1_ASM1670805v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708055.1_ASM1670805v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:30:32,457] [INFO] Task succeeded: fastANI
[2023-06-30 03:30:32,476] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:30:32,476] [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_016720075.1	s__ZC4RG30 sp016720075	98.8456	1040	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	98.74	98.64	0.92	0.90	3	conclusive
GCA_003242275.1	s__ZC4RG30 sp003242275	81.1519	466	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655465.1	s__ZC4RG30 sp015655465	79.8943	390	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903868595.1	s__ZC4RG30 sp903868595	79.4513	364	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	99.92	99.90	0.97	0.96	3	-
GCA_009923475.1	s__UBA964 sp009923475	78.7253	135	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241455.1	s__FEN-1191 sp018241455	78.1987	181	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__FEN-1191	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240525.1	s__13-2-20CM-66-19 sp018240525	78.0923	271	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__13-2-20CM-66-19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707425.1	s__JADJHU01 sp016707425	77.9212	179	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__JADJHU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938365.1	s__UBA964 sp903938365	77.8001	249	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	99.27	99.13	0.88	0.87	4	-
GCA_902826575.1	s__CADEFQ01 sp902826575	77.6648	216	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CADEFQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903908825.1	s__ZC4RG30 sp903908825	77.619	233	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__ZC4RG30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826225.1	s__CADEED01 sp902826225	77.5625	207	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CADEED01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359565.1	s__Immundisolibacter sp014359565	76.6576	153	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Immundisolibacterales;f__Immundisolibacteraceae;g__Immundisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	76.4059	223	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006386545.1	s__Pseudorivibacter rhizosphaerae	76.2239	191	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudorivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003265685.1	s__Piscinibacter caeni	76.1996	246	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011805.1	s__Piscinibacter defluvii	76.1317	253	1095	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 03:30:32,478] [INFO] GTDB search result was written to GCA_016708055.1_ASM1670805v1_genomic.fna/result_gtdb.tsv
[2023-06-30 03:30:32,479] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:30:32,484] [INFO] DFAST_QC result json was written to GCA_016708055.1_ASM1670805v1_genomic.fna/dqc_result.json
[2023-06-30 03:30:32,485] [INFO] DFAST_QC completed!
[2023-06-30 03:30:32,485] [INFO] Total running time: 0h1m25s