[2023-06-18 19:36:27,648] [INFO] DFAST_QC pipeline started.
[2023-06-18 19:36:27,651] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 19:36:27,651] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d304eda-5f0b-40c2-946e-bc247e815b32/dqc_reference
[2023-06-18 19:36:29,861] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 19:36:29,862] [INFO] Task started: Prodigal
[2023-06-18 19:36:29,862] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fc3da0a-1e71-4f88-a79f-6b73aa4a705e/GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 19:36:36,757] [INFO] Task succeeded: Prodigal
[2023-06-18 19:36:36,758] [INFO] Task started: HMMsearch
[2023-06-18 19:36:36,758] [INFO] Running command: hmmsearch --tblout GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d304eda-5f0b-40c2-946e-bc247e815b32/dqc_reference/reference_markers.hmm GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-18 19:36:36,967] [INFO] Task succeeded: HMMsearch
[2023-06-18 19:36:36,968] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8fc3da0a-1e71-4f88-a79f-6b73aa4a705e/GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-18 19:36:36,999] [INFO] Query marker FASTA was written to GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-18 19:36:36,999] [INFO] Task started: Blastn
[2023-06-18 19:36:36,999] [INFO] Running command: blastn -query GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d304eda-5f0b-40c2-946e-bc247e815b32/dqc_reference/reference_markers.fasta -out GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:36:37,841] [INFO] Task succeeded: Blastn
[2023-06-18 19:36:37,846] [INFO] Selected 15 target genomes.
[2023-06-18 19:36:37,846] [INFO] Target genome list was writen to GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-18 19:36:37,849] [INFO] Task started: fastANI
[2023-06-18 19:36:37,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fc3da0a-1e71-4f88-a79f-6b73aa4a705e/GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 19:36:47,533] [INFO] Task succeeded: fastANI
[2023-06-18 19:36:47,534] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d304eda-5f0b-40c2-946e-bc247e815b32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 19:36:47,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d304eda-5f0b-40c2-946e-bc247e815b32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 19:36:47,552] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 19:36:47,552] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 19:36:47,552] [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
Paracoccus luteus	strain=CFH 10530	GCA_004522155.1	2508543	2508543	type	True	84.641	476	651	95	below_threshold
Paracoccus endophyticus	strain=SYSUP0003	GCA_003286075.1	2233774	2233774	type	True	84.044	486	651	95	below_threshold
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	83.1608	440	651	95	below_threshold
Paracoccus solventivorans	strain=DSM 6637	GCA_900142875.1	53463	53463	type	True	82.997	439	651	95	below_threshold
Paracoccus salipaludis	strain=WN007	GCA_002287065.1	2032623	2032623	type	True	82.9342	459	651	95	below_threshold
Paracoccus chinensis	strain=CGMCC 1.7655	GCA_900102885.1	525640	525640	type	True	82.8603	457	651	95	below_threshold
Paracoccus alkenifer	strain=DSM 11593	GCA_900108405.1	65735	65735	type	True	82.3586	426	651	95	below_threshold
Paracoccus contaminans	strain=RKI 16-01929T=LMG 29738T=CCM 8701T=CIP 111112T	GCA_002105555.1	1945662	1945662	type	True	82.2416	415	651	95	below_threshold
Paracoccus sanguinis	strain=DSM 29303	GCA_900106665.1	1545044	1545044	type	True	81.9783	450	651	95	below_threshold
Paracoccus aeridis	strain=JC501	GCA_004923205.2	1966466	1966466	type	True	81.5372	398	651	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	81.3224	402	651	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	80.9079	395	651	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	80.2069	345	651	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.6931	359	651	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.5445	284	651	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 19:36:47,554] [INFO] DFAST Taxonomy check result was written to GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-18 19:36:47,555] [INFO] ===== Taxonomy check completed =====
[2023-06-18 19:36:47,555] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 19:36:47,555] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d304eda-5f0b-40c2-946e-bc247e815b32/dqc_reference/checkm_data
[2023-06-18 19:36:47,556] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 19:36:47,586] [INFO] Task started: CheckM
[2023-06-18 19:36:47,586] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-18 19:37:13,078] [INFO] Task succeeded: CheckM
[2023-06-18 19:37:13,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.45%
Contamintation: 5.56%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 19:37:13,104] [INFO] ===== Completeness check finished =====
[2023-06-18 19:37:13,105] [INFO] ===== Start GTDB Search =====
[2023-06-18 19:37:13,105] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-18 19:37:13,105] [INFO] Task started: Blastn
[2023-06-18 19:37:13,106] [INFO] Running command: blastn -query GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d304eda-5f0b-40c2-946e-bc247e815b32/dqc_reference/reference_markers_gtdb.fasta -out GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 19:37:14,619] [INFO] Task succeeded: Blastn
[2023-06-18 19:37:14,624] [INFO] Selected 11 target genomes.
[2023-06-18 19:37:14,624] [INFO] Target genome list was writen to GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 19:37:14,632] [INFO] Task started: fastANI
[2023-06-18 19:37:14,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fc3da0a-1e71-4f88-a79f-6b73aa4a705e/GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 19:37:22,261] [INFO] Task succeeded: fastANI
[2023-06-18 19:37:22,277] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 19:37:22,278] [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_004522155.1	s__Paracoccus luteus	84.6552	476	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003286075.1	s__Paracoccus endophyticus	84.0247	487	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763805.1	s__Paracoccus sphaerophysae	83.0691	445	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142875.1	s__Paracoccus solventivorans	83.0102	438	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.61	95.99	0.87	0.87	3	-
GCF_002287065.1	s__Paracoccus salipaludis	82.9653	457	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102885.1	s__Paracoccus chinensis	82.8788	456	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016617715.1	s__Paracoccus sp014164625	82.82	475	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.50	99.01	0.95	0.90	3	-
GCF_900108405.1	s__Paracoccus alkenifer	82.3636	425	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105555.1	s__Paracoccus contaminans	82.2605	414	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007018965.1	s__Paracoccus marinus	81.8511	399	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923205.2	s__Paracoccus aeridis	81.5276	398	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 19:37:22,280] [INFO] GTDB search result was written to GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-18 19:37:22,280] [INFO] ===== GTDB Search completed =====
[2023-06-18 19:37:22,287] [INFO] DFAST_QC result json was written to GCA_937859005.1_SRR1763383_bin.83_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-18 19:37:22,287] [INFO] DFAST_QC completed!
[2023-06-18 19:37:22,288] [INFO] Total running time: 0h0m55s