[2024-01-24 12:13:58,984] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:58,985] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:58,986] [INFO] DQC Reference Directory: /var/lib/cwl/stg583de1fa-94f6-4ce9-9a21-d96c097a423e/dqc_reference
[2024-01-24 12:14:00,502] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:00,503] [INFO] Task started: Prodigal
[2024-01-24 12:14:00,503] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a842da2-de68-4283-b1d7-1d8e0cc6d245/GCF_019740335.1_ASM1974033v1_genomic.fna.gz | prodigal -d GCF_019740335.1_ASM1974033v1_genomic.fna/cds.fna -a GCF_019740335.1_ASM1974033v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:11,247] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:11,247] [INFO] Task started: HMMsearch
[2024-01-24 12:14:11,247] [INFO] Running command: hmmsearch --tblout GCF_019740335.1_ASM1974033v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg583de1fa-94f6-4ce9-9a21-d96c097a423e/dqc_reference/reference_markers.hmm GCF_019740335.1_ASM1974033v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:11,549] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:11,550] [INFO] Found 6/6 markers.
[2024-01-24 12:14:11,600] [INFO] Query marker FASTA was written to GCF_019740335.1_ASM1974033v1_genomic.fna/markers.fasta
[2024-01-24 12:14:11,600] [INFO] Task started: Blastn
[2024-01-24 12:14:11,600] [INFO] Running command: blastn -query GCF_019740335.1_ASM1974033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg583de1fa-94f6-4ce9-9a21-d96c097a423e/dqc_reference/reference_markers.fasta -out GCF_019740335.1_ASM1974033v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:12,459] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:12,462] [INFO] Selected 26 target genomes.
[2024-01-24 12:14:12,462] [INFO] Target genome list was writen to GCF_019740335.1_ASM1974033v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:12,472] [INFO] Task started: fastANI
[2024-01-24 12:14:12,472] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a842da2-de68-4283-b1d7-1d8e0cc6d245/GCF_019740335.1_ASM1974033v1_genomic.fna.gz --refList GCF_019740335.1_ASM1974033v1_genomic.fna/target_genomes.txt --output GCF_019740335.1_ASM1974033v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:30,785] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:30,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg583de1fa-94f6-4ce9-9a21-d96c097a423e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:30,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg583de1fa-94f6-4ce9-9a21-d96c097a423e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:30,806] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:30,806] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:30,806] [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
Aquisediminimonas sediminicola	strain=CH68-4	GCA_019740335.1	2676787	2676787	type	True	100.0	998	998	95	conclusive
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	77.6542	214	998	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_000445145.1	1332080	1332080	type	True	77.5168	195	998	95	below_threshold
Sphingobium fontiphilum	strain=DSM 29348	GCA_014196635.1	944425	944425	type	True	77.5164	218	998	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	77.489	193	998	95	below_threshold
Sphingobium herbicidovorans	strain=NBRC 16415	GCA_001598535.1	76947	76947	type	True	77.4134	160	998	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	77.3757	200	998	95	below_threshold
Sphingobium herbicidovorans	strain=NBRC 16415	GCA_000632125.2	76947	76947	type	True	77.3731	163	998	95	below_threshold
Sphingobium herbicidovorans	strain=MH	GCA_002080435.1	76947	76947	type	True	77.3686	162	998	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	77.3618	215	998	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	77.3035	178	998	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	77.2554	213	998	95	below_threshold
Sphingomonas asaccharolytica	strain=NBRC 15499	GCA_001598355.1	40681	40681	type	True	77.2409	153	998	95	below_threshold
Sphingomonas montana	strain=W16RD	GCA_001956315.1	1843236	1843236	type	True	77.1767	154	998	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.1665	177	998	95	below_threshold
Sphingomonas pruni	strain=NBRC 15498	GCA_001598455.1	40683	40683	type	True	77.1594	167	998	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	77.1061	172	998	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	77.1002	172	998	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.077	193	998	95	below_threshold
Sphingomonas crusticola	strain=MIMD3	GCA_003391115.1	1697973	1697973	type	True	77.0557	149	998	95	below_threshold
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	77.0506	182	998	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	76.9999	199	998	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	76.9602	178	998	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	76.8767	159	998	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	76.4795	82	998	95	below_threshold
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	76.4722	102	998	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:30,808] [INFO] DFAST Taxonomy check result was written to GCF_019740335.1_ASM1974033v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:30,810] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:30,810] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:30,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg583de1fa-94f6-4ce9-9a21-d96c097a423e/dqc_reference/checkm_data
[2024-01-24 12:14:30,812] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:30,857] [INFO] Task started: CheckM
[2024-01-24 12:14:30,857] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019740335.1_ASM1974033v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019740335.1_ASM1974033v1_genomic.fna/checkm_input GCF_019740335.1_ASM1974033v1_genomic.fna/checkm_result
[2024-01-24 12:15:05,225] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:05,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:05,254] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:05,254] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:05,255] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019740335.1_ASM1974033v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:05,255] [INFO] Task started: Blastn
[2024-01-24 12:15:05,255] [INFO] Running command: blastn -query GCF_019740335.1_ASM1974033v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg583de1fa-94f6-4ce9-9a21-d96c097a423e/dqc_reference/reference_markers_gtdb.fasta -out GCF_019740335.1_ASM1974033v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:06,749] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:06,752] [INFO] Selected 22 target genomes.
[2024-01-24 12:15:06,752] [INFO] Target genome list was writen to GCF_019740335.1_ASM1974033v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:06,783] [INFO] Task started: fastANI
[2024-01-24 12:15:06,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a842da2-de68-4283-b1d7-1d8e0cc6d245/GCF_019740335.1_ASM1974033v1_genomic.fna.gz --refList GCF_019740335.1_ASM1974033v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019740335.1_ASM1974033v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:21,674] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:21,699] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:15:21,699] [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_002422945.1	s__UBA6174 sp002422945	91.5084	648	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__UBA6174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903821605.1	s__UBA6174 sp903821605	81.6123	481	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__UBA6174	95.0	99.98	99.98	0.97	0.97	2	-
GCF_002151445.1	s__Sphingomonas_E sp002151445	77.7979	234	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000744515.1	s__Rhizorhabdus wittichii_A	77.7269	200	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034225.1	s__Sphingomonas_E fennica	77.6542	214	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	98.08	97.94	0.82	0.81	3	-
GCF_900101455.1	s__Rhizorhabdus sp900101455	77.6455	198	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011044255.1	s__Rhizorhabdus sp011044255	77.3035	178	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001563285.1	s__Sphingobium sp001563285	77.2701	163	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008692605.1	s__Sphingobium estronivorans	77.2554	213	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598355.1	s__Sphingomonas asaccharolytica	77.2418	153	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015693305.1	s__Sphingobium sp015693305	77.2013	166	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457415.1	s__Sphingobium sp002457415	77.1723	193	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590775.1	s__Sphingobium_A sp003590775	77.1665	177	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598455.1	s__Sphingomonas pruni	77.1594	167	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762195.1	s__Sphingomonas_N oligoaromativorans	77.1078	172	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003391115.1	s__Sphingomonas_I crusticola	77.0557	149	998	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_003515075.1	s__Sphingomonas gilva	77.0253	171	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149295.1	s__Novosphingobium sp013149295	76.972	197	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004005905.1	s__Novosphingobium umbonatum	76.9608	177	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018006725.1	s__Rhizorhabdus sp018006725	76.9585	184	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127225.1	s__Sphingomonas sp002127225	76.9154	178	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903644055.1	s__Sphingomonas_I sp903644055	76.4865	113	998	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:21,701] [INFO] GTDB search result was written to GCF_019740335.1_ASM1974033v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:21,703] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:21,708] [INFO] DFAST_QC result json was written to GCF_019740335.1_ASM1974033v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:21,708] [INFO] DFAST_QC completed!
[2024-01-24 12:15:21,708] [INFO] Total running time: 0h1m23s