[2023-06-05 18:42:27,997] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:42:27,998] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:42:27,999] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4fa6206-4180-4816-9e11-daa47898a14f/dqc_reference
[2023-06-05 18:42:29,113] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:42:29,114] [INFO] Task started: Prodigal
[2023-06-05 18:42:29,114] [INFO] Running command: gunzip -c /var/lib/cwl/stg26732904-8ef1-4f43-87e7-5cc951c41e94/GCA_934560975.1_ERR7747324_bin.278_genomic.fna.gz | prodigal -d GCA_934560975.1_ERR7747324_bin.278_genomic.fna/cds.fna -a GCA_934560975.1_ERR7747324_bin.278_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:42:37,415] [INFO] Task succeeded: Prodigal
[2023-06-05 18:42:37,415] [INFO] Task started: HMMsearch
[2023-06-05 18:42:37,415] [INFO] Running command: hmmsearch --tblout GCA_934560975.1_ERR7747324_bin.278_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4fa6206-4180-4816-9e11-daa47898a14f/dqc_reference/reference_markers.hmm GCA_934560975.1_ERR7747324_bin.278_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:42:37,618] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:42:37,619] [INFO] Found 6/6 markers.
[2023-06-05 18:42:37,645] [INFO] Query marker FASTA was written to GCA_934560975.1_ERR7747324_bin.278_genomic.fna/markers.fasta
[2023-06-05 18:42:37,645] [INFO] Task started: Blastn
[2023-06-05 18:42:37,645] [INFO] Running command: blastn -query GCA_934560975.1_ERR7747324_bin.278_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4fa6206-4180-4816-9e11-daa47898a14f/dqc_reference/reference_markers.fasta -out GCA_934560975.1_ERR7747324_bin.278_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:42:38,500] [INFO] Task succeeded: Blastn
[2023-06-05 18:42:38,504] [INFO] Selected 28 target genomes.
[2023-06-05 18:42:38,504] [INFO] Target genome list was writen to GCA_934560975.1_ERR7747324_bin.278_genomic.fna/target_genomes.txt
[2023-06-05 18:42:38,519] [INFO] Task started: fastANI
[2023-06-05 18:42:38,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg26732904-8ef1-4f43-87e7-5cc951c41e94/GCA_934560975.1_ERR7747324_bin.278_genomic.fna.gz --refList GCA_934560975.1_ERR7747324_bin.278_genomic.fna/target_genomes.txt --output GCA_934560975.1_ERR7747324_bin.278_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:43:04,723] [INFO] Task succeeded: fastANI
[2023-06-05 18:43:04,724] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4fa6206-4180-4816-9e11-daa47898a14f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:43:04,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4fa6206-4180-4816-9e11-daa47898a14f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:43:04,743] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:43:04,743] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:43:04,744] [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
Sphingomonas crusticola	strain=MIMD3	GCA_003391115.1	1697973	1697973	type	True	79.7983	454	1016	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	79.3116	416	1016	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	79.2318	437	1016	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	79.165	384	1016	95	below_threshold
Sphingomonas vulcanisoli	strain=CECT 8804	GCA_011761305.1	1658060	1658060	type	True	79.0873	366	1016	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	79.0776	405	1016	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	78.8877	364	1016	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	78.7841	363	1016	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	78.7735	394	1016	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	78.7483	366	1016	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	78.7475	394	1016	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.6991	426	1016	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	78.6021	367	1016	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.4434	388	1016	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.3425	325	1016	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	78.2564	414	1016	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.2112	329	1016	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	78.1931	303	1016	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	78.1481	357	1016	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.1344	403	1016	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	78.0108	264	1016	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.8406	273	1016	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	77.7919	314	1016	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	75.7097	85	1016	95	below_threshold
Rhizobium fabae	strain=CCBAU 33202	GCA_003985135.1	573179	573179	type	True	75.6044	104	1016	95	below_threshold
Rhizobium fabae	strain=DSM 19331	GCA_014196235.1	573179	573179	type	True	75.5918	105	1016	95	below_threshold
Rhizobium indigoferae	strain=CCBAU 71042	GCA_013087605.1	158891	158891	type	True	75.5337	87	1016	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_003058385.1	384	384	suspected-type	True	75.4901	101	1016	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:43:04,745] [INFO] DFAST Taxonomy check result was written to GCA_934560975.1_ERR7747324_bin.278_genomic.fna/tc_result.tsv
[2023-06-05 18:43:04,746] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:43:04,746] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:43:04,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4fa6206-4180-4816-9e11-daa47898a14f/dqc_reference/checkm_data
[2023-06-05 18:43:04,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:43:04,781] [INFO] Task started: CheckM
[2023-06-05 18:43:04,781] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934560975.1_ERR7747324_bin.278_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934560975.1_ERR7747324_bin.278_genomic.fna/checkm_input GCA_934560975.1_ERR7747324_bin.278_genomic.fna/checkm_result
[2023-06-05 18:43:33,936] [INFO] Task succeeded: CheckM
[2023-06-05 18:43:33,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:43:33,955] [INFO] ===== Completeness check finished =====
[2023-06-05 18:43:33,955] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:43:33,956] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934560975.1_ERR7747324_bin.278_genomic.fna/markers.fasta)
[2023-06-05 18:43:33,957] [INFO] Task started: Blastn
[2023-06-05 18:43:33,957] [INFO] Running command: blastn -query GCA_934560975.1_ERR7747324_bin.278_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4fa6206-4180-4816-9e11-daa47898a14f/dqc_reference/reference_markers_gtdb.fasta -out GCA_934560975.1_ERR7747324_bin.278_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:43:35,568] [INFO] Task succeeded: Blastn
[2023-06-05 18:43:35,577] [INFO] Selected 28 target genomes.
[2023-06-05 18:43:35,577] [INFO] Target genome list was writen to GCA_934560975.1_ERR7747324_bin.278_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:43:35,828] [INFO] Task started: fastANI
[2023-06-05 18:43:35,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg26732904-8ef1-4f43-87e7-5cc951c41e94/GCA_934560975.1_ERR7747324_bin.278_genomic.fna.gz --refList GCA_934560975.1_ERR7747324_bin.278_genomic.fna/target_genomes_gtdb.txt --output GCA_934560975.1_ERR7747324_bin.278_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:43:57,140] [INFO] Task succeeded: fastANI
[2023-06-05 18:43:57,157] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:43:57,157] [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_003391115.1	s__Sphingomonas_I crusticola	79.8102	453	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013113735.1	s__Sphingomonas_I sp013113735	79.6017	482	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248515.1	s__Sphingomonas_I sp003248515	79.2463	443	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903644055.1	s__Sphingomonas_I sp903644055	79.2145	309	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050615.1	s__Sphingomonas_H oleivorans	79.1423	386	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	79.0328	409	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188165.1	s__Sphingomonas_E laterariae	78.8579	367	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341505.2	s__Sphingomonas sp004341505	78.7976	368	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_004135605.1	s__Sphingomonas desiccabilis	78.7716	364	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004005865.1	s__Rhizorhabdus crocodyli	78.6488	366	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114095.1	s__Sphingomonas sp900114095	78.4009	395	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409985.1	s__Sphingomonas melonis_A	78.3918	416	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009913435.1	s__Sphingomonas_B sp009913435	78.3773	322	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012035195.1	s__Sphingomonas sp012035195	78.3733	395	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009753715.1	s__Sphingomonas_B horti	78.3155	326	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011927695.1	s__Sphingomonas_K jejuensis	78.229	300	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004796535.1	s__Sphingomonas_L sp004796535	78.2115	329	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013328205.1	s__Sphingomonas hominis	78.1192	331	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974765.1	s__Sphingomonas_B changbaiensis	78.0625	309	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291855.1	s__Sphingomonas_B sp002291855	78.056	252	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000711715.1	s__Sphingomicrobium astaxanthinifaciens	78.0108	219	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873375.1	s__Sphingomicrobium sp014873375	77.827	158	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005144715.1	s__Sphingomonas sp005144715	77.7915	314	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016743815.1	s__Sphingomonas sp016743815	77.6288	302	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	77.565	205	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115295.1	s__Sphingomonas sp900115295	77.4828	301	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506425.1	s__Novosphingobium sp902506425	77.3915	233	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204535.1	s__Novosphingobium chloroacetimidivorans	77.3776	251	1016	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:43:57,160] [INFO] GTDB search result was written to GCA_934560975.1_ERR7747324_bin.278_genomic.fna/result_gtdb.tsv
[2023-06-05 18:43:57,160] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:43:57,183] [INFO] DFAST_QC result json was written to GCA_934560975.1_ERR7747324_bin.278_genomic.fna/dqc_result.json
[2023-06-05 18:43:57,183] [INFO] DFAST_QC completed!
[2023-06-05 18:43:57,183] [INFO] Total running time: 0h1m29s