[2024-01-24 13:16:56,209] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:16:56,210] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:16:56,210] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc327f76-7acd-45db-a69c-b743e732415b/dqc_reference
[2024-01-24 13:16:57,373] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:16:57,374] [INFO] Task started: Prodigal
[2024-01-24 13:16:57,374] [INFO] Running command: gunzip -c /var/lib/cwl/stge1145eda-bed3-4bdd-bdf9-210aba432044/GCF_011044255.1_ASM1104425v1_genomic.fna.gz | prodigal -d GCF_011044255.1_ASM1104425v1_genomic.fna/cds.fna -a GCF_011044255.1_ASM1104425v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:09,618] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:09,619] [INFO] Task started: HMMsearch
[2024-01-24 13:17:09,619] [INFO] Running command: hmmsearch --tblout GCF_011044255.1_ASM1104425v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc327f76-7acd-45db-a69c-b743e732415b/dqc_reference/reference_markers.hmm GCF_011044255.1_ASM1104425v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:09,897] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:09,898] [INFO] Found 6/6 markers.
[2024-01-24 13:17:09,950] [INFO] Query marker FASTA was written to GCF_011044255.1_ASM1104425v1_genomic.fna/markers.fasta
[2024-01-24 13:17:09,951] [INFO] Task started: Blastn
[2024-01-24 13:17:09,951] [INFO] Running command: blastn -query GCF_011044255.1_ASM1104425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc327f76-7acd-45db-a69c-b743e732415b/dqc_reference/reference_markers.fasta -out GCF_011044255.1_ASM1104425v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:10,944] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:10,948] [INFO] Selected 16 target genomes.
[2024-01-24 13:17:10,949] [INFO] Target genome list was writen to GCF_011044255.1_ASM1104425v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:10,958] [INFO] Task started: fastANI
[2024-01-24 13:17:10,958] [INFO] Running command: fastANI --query /var/lib/cwl/stge1145eda-bed3-4bdd-bdf9-210aba432044/GCF_011044255.1_ASM1104425v1_genomic.fna.gz --refList GCF_011044255.1_ASM1104425v1_genomic.fna/target_genomes.txt --output GCF_011044255.1_ASM1104425v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:25,557] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:25,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc327f76-7acd-45db-a69c-b743e732415b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:25,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc327f76-7acd-45db-a69c-b743e732415b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:25,571] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:25,571] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:25,572] [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
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	100.0	1442	1442	95	conclusive
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	82.3367	836	1442	95	below_threshold
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	82.1325	732	1442	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	79.2816	473	1442	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	79.2792	425	1442	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	79.2221	500	1442	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	79.0385	465	1442	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	79.0081	513	1442	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	78.7809	446	1442	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.7682	369	1442	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.5617	368	1442	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	78.5169	421	1442	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	78.3339	425	1442	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.2742	437	1442	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.1849	358	1442	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.0199	365	1442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:25,573] [INFO] DFAST Taxonomy check result was written to GCF_011044255.1_ASM1104425v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:25,573] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:25,574] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:25,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc327f76-7acd-45db-a69c-b743e732415b/dqc_reference/checkm_data
[2024-01-24 13:17:25,575] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:25,625] [INFO] Task started: CheckM
[2024-01-24 13:17:25,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011044255.1_ASM1104425v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011044255.1_ASM1104425v1_genomic.fna/checkm_input GCF_011044255.1_ASM1104425v1_genomic.fna/checkm_result
[2024-01-24 13:18:05,709] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:05,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:05,734] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:05,734] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:05,735] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011044255.1_ASM1104425v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:05,735] [INFO] Task started: Blastn
[2024-01-24 13:18:05,735] [INFO] Running command: blastn -query GCF_011044255.1_ASM1104425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc327f76-7acd-45db-a69c-b743e732415b/dqc_reference/reference_markers_gtdb.fasta -out GCF_011044255.1_ASM1104425v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:07,643] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:07,648] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:07,648] [INFO] Target genome list was writen to GCF_011044255.1_ASM1104425v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:07,656] [INFO] Task started: fastANI
[2024-01-24 13:18:07,656] [INFO] Running command: fastANI --query /var/lib/cwl/stge1145eda-bed3-4bdd-bdf9-210aba432044/GCF_011044255.1_ASM1104425v1_genomic.fna.gz --refList GCF_011044255.1_ASM1104425v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011044255.1_ASM1104425v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:17,663] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:17,675] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:17,675] [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_011044255.1	s__Rhizorhabdus sp011044255	100.0	1442	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018006725.1	s__Rhizorhabdus sp018006725	87.4864	987	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016765.1	s__Rhizorhabdus wittichii	82.9799	847	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_001428605.1	s__Rhizorhabdus sp001428605	82.5117	796	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.98	99.98	0.99	0.99	3	-
GCF_900167915.1	s__Rhizorhabdus histidinilytica	82.3429	837	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.24	99.18	0.90	0.89	3	-
GCF_002355275.1	s__Rhizorhabdus dicambivorans	82.1436	731	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.99	99.99	1.00	0.99	3	-
GCF_001015195.1	s__Rhizorhabdus sp001015195	81.8823	735	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297635.1	s__Rhizorhabdus sp004297635	81.3929	373	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.78	98.78	0.98	0.98	2	-
GCF_900101455.1	s__Rhizorhabdus sp900101455	79.4794	490	1442	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	79.2417	477	1442	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	98.08	97.94	0.82	0.81	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:17,677] [INFO] GTDB search result was written to GCF_011044255.1_ASM1104425v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:17,677] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:17,681] [INFO] DFAST_QC result json was written to GCF_011044255.1_ASM1104425v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:17,681] [INFO] DFAST_QC completed!
[2024-01-24 13:18:17,681] [INFO] Total running time: 0h1m21s