[2024-01-24 11:58:57,014] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,016] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,017] [INFO] DQC Reference Directory: /var/lib/cwl/stgf10868d8-06f0-424a-8465-93667e62b8fd/dqc_reference
[2024-01-24 11:58:58,353] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,354] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,354] [INFO] Running command: gunzip -c /var/lib/cwl/stg19e01cb3-4f0b-429f-8bdd-483fb8cc6a22/GCF_022569295.1_ASM2256929v1_genomic.fna.gz | prodigal -d GCF_022569295.1_ASM2256929v1_genomic.fna/cds.fna -a GCF_022569295.1_ASM2256929v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:09,806] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:09,806] [INFO] Task started: HMMsearch
[2024-01-24 11:59:09,806] [INFO] Running command: hmmsearch --tblout GCF_022569295.1_ASM2256929v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf10868d8-06f0-424a-8465-93667e62b8fd/dqc_reference/reference_markers.hmm GCF_022569295.1_ASM2256929v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:10,096] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:10,097] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg19e01cb3-4f0b-429f-8bdd-483fb8cc6a22/GCF_022569295.1_ASM2256929v1_genomic.fna.gz]
[2024-01-24 11:59:10,136] [INFO] Query marker FASTA was written to GCF_022569295.1_ASM2256929v1_genomic.fna/markers.fasta
[2024-01-24 11:59:10,136] [INFO] Task started: Blastn
[2024-01-24 11:59:10,136] [INFO] Running command: blastn -query GCF_022569295.1_ASM2256929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf10868d8-06f0-424a-8465-93667e62b8fd/dqc_reference/reference_markers.fasta -out GCF_022569295.1_ASM2256929v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:11,133] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:11,141] [INFO] Selected 25 target genomes.
[2024-01-24 11:59:11,141] [INFO] Target genome list was writen to GCF_022569295.1_ASM2256929v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:11,151] [INFO] Task started: fastANI
[2024-01-24 11:59:11,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg19e01cb3-4f0b-429f-8bdd-483fb8cc6a22/GCF_022569295.1_ASM2256929v1_genomic.fna.gz --refList GCF_022569295.1_ASM2256929v1_genomic.fna/target_genomes.txt --output GCF_022569295.1_ASM2256929v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:29,475] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:29,476] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf10868d8-06f0-424a-8465-93667e62b8fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:29,476] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf10868d8-06f0-424a-8465-93667e62b8fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:29,494] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:29,494] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:29,495] [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
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	100.0	1207	1209	95	conclusive
Hankyongella ginsenosidimutans	strain=W1-2-3	GCA_005144965.1	1763828	1763828	type	True	78.1662	259	1209	95	below_threshold
Novosphingobium fuchskuhlense	strain=FNE08-7	GCA_001519075.1	1117702	1117702	type	True	77.5739	156	1209	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	77.5569	258	1209	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	77.3474	214	1209	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	77.2685	235	1209	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	77.2612	199	1209	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	77.2581	254	1209	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	77.2552	235	1209	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.1249	215	1209	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.1156	211	1209	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	77.1026	254	1209	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	77.0436	216	1209	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	77.0019	234	1209	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	76.9883	176	1209	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	76.9724	220	1209	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	76.9569	200	1209	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	76.8861	148	1209	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	76.8321	160	1209	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.8098	157	1209	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	76.793	209	1209	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	76.714	156	1209	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014197855.1	140057	140057	type	True	76.6642	144	1209	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	76.6358	146	1209	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	76.515	185	1209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:29,496] [INFO] DFAST Taxonomy check result was written to GCF_022569295.1_ASM2256929v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:29,497] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:29,497] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:29,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf10868d8-06f0-424a-8465-93667e62b8fd/dqc_reference/checkm_data
[2024-01-24 11:59:29,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:29,536] [INFO] Task started: CheckM
[2024-01-24 11:59:29,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022569295.1_ASM2256929v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022569295.1_ASM2256929v1_genomic.fna/checkm_input GCF_022569295.1_ASM2256929v1_genomic.fna/checkm_result
[2024-01-24 12:00:05,955] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:05,956] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:05,981] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:05,981] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:05,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022569295.1_ASM2256929v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:05,982] [INFO] Task started: Blastn
[2024-01-24 12:00:05,982] [INFO] Running command: blastn -query GCF_022569295.1_ASM2256929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf10868d8-06f0-424a-8465-93667e62b8fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_022569295.1_ASM2256929v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:07,902] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:07,905] [INFO] Selected 28 target genomes.
[2024-01-24 12:00:07,906] [INFO] Target genome list was writen to GCF_022569295.1_ASM2256929v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:07,925] [INFO] Task started: fastANI
[2024-01-24 12:00:07,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg19e01cb3-4f0b-429f-8bdd-483fb8cc6a22/GCF_022569295.1_ASM2256929v1_genomic.fna.gz --refList GCF_022569295.1_ASM2256929v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022569295.1_ASM2256929v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:27,523] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:27,545] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:00:27,546] [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_005144965.1	s__Hankyongella ginsenosidimutans	78.1952	257	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Hankyongella	95.0	98.05	98.05	0.80	0.80	2	-
GCF_001519075.1	s__Novosphingobium fuchskuhlense	77.5739	156	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001890385.1	s__Tardibacter chloracetimidivorans	77.4213	162	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tardibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744835.1	s__Sphingomonas sp017744835	77.3344	200	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009733735.1	s__Sandarakinorhabdus oryzae	77.3055	173	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sandarakinorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	77.2617	199	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135605.1	s__Sphingomonas desiccabilis	77.2552	235	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003130795.1	s__Azospirillum thermophilum	77.1253	254	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003345355.1	s__Sphingomonas sp003345355	77.1245	215	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702385.1	s__Xanthobacter sp000702385	77.1112	220	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	96.09	96.09	0.89	0.89	2	-
GCF_004135585.1	s__Allosphingosinicella sp004135585	77.0736	180	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167915.1	s__Rhizorhabdus histidinilytica	77.0702	236	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.24	99.18	0.90	0.89	3	-
GCF_017876165.1	s__Azospirillum soli	77.056	215	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129465.1	s__Allosphingosinicella humi	77.0453	195	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010525.1	s__Azorhizobium caulinodans	77.0033	217	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	97.54	97.54	0.94	0.94	2	-
GCF_009789575.1	s__Stappia indica_A	76.9981	179	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696535.1	s__Stappia indica	76.965	176	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	97.23	96.79	0.94	0.94	3	-
GCF_004152845.1	s__Sphingobium fuliginis	76.9601	198	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.53	97.80	0.87	0.78	14	-
GCF_017876155.1	s__Azospirillum rugosum	76.9486	249	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248935.1	s__Sphingobium sp003248935	76.928	171	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820445.1	s__Sphingomonas sp016820445	76.9166	182	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.21	97.21	0.90	0.90	2	-
GCF_014206975.1	s__Aminobacter aganoensis	76.8534	150	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.80	98.79	0.89	0.89	3	-
GCF_016629525.1	s__Kaistia sp016629525	76.7648	160	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	76.738	209	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_001591025.1	s__Sphingomonas soli	76.7272	155	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349955.1	s__Azospirillum brasilense_B	76.7202	245	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCA_003243195.1	s__Sphingomonas taxi_B	76.6606	208	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185715.1	s__Bosea sp900185715	76.6418	173	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:27,547] [INFO] GTDB search result was written to GCF_022569295.1_ASM2256929v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:27,548] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:27,553] [INFO] DFAST_QC result json was written to GCF_022569295.1_ASM2256929v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:27,554] [INFO] DFAST_QC completed!
[2024-01-24 12:00:27,554] [INFO] Total running time: 0h1m31s