[2024-01-25 18:03:50,841] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:50,843] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:50,843] [INFO] DQC Reference Directory: /var/lib/cwl/stgb63e78a3-afb4-4312-ad45-74c341a0157f/dqc_reference
[2024-01-25 18:03:51,963] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:51,963] [INFO] Task started: Prodigal
[2024-01-25 18:03:51,964] [INFO] Running command: gunzip -c /var/lib/cwl/stg30f418a1-7d60-4d54-8d65-eaeed270080c/GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna.gz | prodigal -d GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/cds.fna -a GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:04:02,841] [INFO] Task succeeded: Prodigal
[2024-01-25 18:04:02,841] [INFO] Task started: HMMsearch
[2024-01-25 18:04:02,841] [INFO] Running command: hmmsearch --tblout GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb63e78a3-afb4-4312-ad45-74c341a0157f/dqc_reference/reference_markers.hmm GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:04:03,066] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:04:03,068] [INFO] Found 6/6 markers.
[2024-01-25 18:04:03,104] [INFO] Query marker FASTA was written to GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta
[2024-01-25 18:04:03,105] [INFO] Task started: Blastn
[2024-01-25 18:04:03,105] [INFO] Running command: blastn -query GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stgb63e78a3-afb4-4312-ad45-74c341a0157f/dqc_reference/reference_markers.fasta -out GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:04,073] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:04,075] [INFO] Selected 15 target genomes.
[2024-01-25 18:04:04,076] [INFO] Target genome list was writen to GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt
[2024-01-25 18:04:04,088] [INFO] Task started: fastANI
[2024-01-25 18:04:04,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg30f418a1-7d60-4d54-8d65-eaeed270080c/GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/target_genomes.txt --output GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:18,085] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:18,085] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb63e78a3-afb4-4312-ad45-74c341a0157f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:18,085] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb63e78a3-afb4-4312-ad45-74c341a0157f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:18,095] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:04:18,095] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:04:18,095] [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
Roseivivax halodurans	strain=JCM 10272	GCA_000521785.1	93683	93683	type	True	100.0	1427	1433	95	conclusive
Roseivivax jejudonensis	strain=CECT 8625	GCA_900172265.1	1529041	1529041	type	True	81.8679	799	1433	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	81.7975	816	1433	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	81.7529	782	1433	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	80.3477	669	1433	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	79.7568	604	1433	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.6341	413	1433	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.5105	416	1433	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.4676	452	1433	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	78.4378	421	1433	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.377	476	1433	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.3518	472	1433	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.3387	475	1433	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.2916	508	1433	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.0295	334	1433	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:18,096] [INFO] DFAST Taxonomy check result was written to GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/tc_result.tsv
[2024-01-25 18:04:18,097] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:18,097] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:18,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb63e78a3-afb4-4312-ad45-74c341a0157f/dqc_reference/checkm_data
[2024-01-25 18:04:18,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:18,140] [INFO] Task started: CheckM
[2024-01-25 18:04:18,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/checkm_input GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/checkm_result
[2024-01-25 18:04:53,607] [INFO] Task succeeded: CheckM
[2024-01-25 18:04:53,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:04:53,655] [INFO] ===== Completeness check finished =====
[2024-01-25 18:04:53,656] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:04:53,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta)
[2024-01-25 18:04:53,656] [INFO] Task started: Blastn
[2024-01-25 18:04:53,656] [INFO] Running command: blastn -query GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/markers.fasta -db /var/lib/cwl/stgb63e78a3-afb4-4312-ad45-74c341a0157f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:55,606] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:55,608] [INFO] Selected 11 target genomes.
[2024-01-25 18:04:55,609] [INFO] Target genome list was writen to GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:04:55,636] [INFO] Task started: fastANI
[2024-01-25 18:04:55,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg30f418a1-7d60-4d54-8d65-eaeed270080c/GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna.gz --refList GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/target_genomes_gtdb.txt --output GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:06,947] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:06,954] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:06,954] [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_000521785.1	s__Roseivivax halodurans	100.0	1427	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900112685.1	s__Roseivivax sediminis	82.3214	822	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172265.1	s__Roseivivax jejudonensis	81.8829	797	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	81.81	815	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109705.1	s__Roseivivax marinus	81.7645	782	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	97.84	97.84	0.91	0.91	2	-
GCF_001482405.1	s__Ponticoccus marisrubri	79.7404	586	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	79.1084	539	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	79.0964	517	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	79.0863	553	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169415.1	s__Sagittula stellata	78.5516	481	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	78.4003	474	1433	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:06,956] [INFO] GTDB search result was written to GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:06,956] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:06,959] [INFO] DFAST_QC result json was written to GCF_000521785.1_SOAPdenovo_v1.05_genomic.fna/dqc_result.json
[2024-01-25 18:05:06,959] [INFO] DFAST_QC completed!
[2024-01-25 18:05:06,959] [INFO] Total running time: 0h1m16s