[2023-06-18 23:43:19,144] [INFO] DFAST_QC pipeline started.
[2023-06-18 23:43:19,153] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 23:43:19,153] [INFO] DQC Reference Directory: /var/lib/cwl/stg0702213c-6e5f-467d-a0a4-3ccd46670187/dqc_reference
[2023-06-18 23:43:20,821] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 23:43:20,822] [INFO] Task started: Prodigal
[2023-06-18 23:43:20,822] [INFO] Running command: gunzip -c /var/lib/cwl/stg56cfb723-c53b-416d-bd4e-4a9a0499f989/GCA_018820025.1_ASM1882002v1_genomic.fna.gz | prodigal -d GCA_018820025.1_ASM1882002v1_genomic.fna/cds.fna -a GCA_018820025.1_ASM1882002v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 23:43:29,913] [INFO] Task succeeded: Prodigal
[2023-06-18 23:43:29,914] [INFO] Task started: HMMsearch
[2023-06-18 23:43:29,914] [INFO] Running command: hmmsearch --tblout GCA_018820025.1_ASM1882002v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0702213c-6e5f-467d-a0a4-3ccd46670187/dqc_reference/reference_markers.hmm GCA_018820025.1_ASM1882002v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 23:43:30,249] [INFO] Task succeeded: HMMsearch
[2023-06-18 23:43:30,250] [INFO] Found 6/6 markers.
[2023-06-18 23:43:30,287] [INFO] Query marker FASTA was written to GCA_018820025.1_ASM1882002v1_genomic.fna/markers.fasta
[2023-06-18 23:43:30,287] [INFO] Task started: Blastn
[2023-06-18 23:43:30,288] [INFO] Running command: blastn -query GCA_018820025.1_ASM1882002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0702213c-6e5f-467d-a0a4-3ccd46670187/dqc_reference/reference_markers.fasta -out GCA_018820025.1_ASM1882002v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:43:30,974] [INFO] Task succeeded: Blastn
[2023-06-18 23:43:30,978] [INFO] Selected 12 target genomes.
[2023-06-18 23:43:30,978] [INFO] Target genome list was writen to GCA_018820025.1_ASM1882002v1_genomic.fna/target_genomes.txt
[2023-06-18 23:43:30,980] [INFO] Task started: fastANI
[2023-06-18 23:43:30,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg56cfb723-c53b-416d-bd4e-4a9a0499f989/GCA_018820025.1_ASM1882002v1_genomic.fna.gz --refList GCA_018820025.1_ASM1882002v1_genomic.fna/target_genomes.txt --output GCA_018820025.1_ASM1882002v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 23:43:42,097] [INFO] Task succeeded: fastANI
[2023-06-18 23:43:42,097] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0702213c-6e5f-467d-a0a4-3ccd46670187/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 23:43:42,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0702213c-6e5f-467d-a0a4-3ccd46670187/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 23:43:42,107] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-06-18 23:43:42,107] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 23:43:42,107] [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
Marinomonas polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	97.664	1151	1265	95	conclusive
Marinomonas lutimaris	strain=E165	GCA_019426345.1	2846746	2846746	type	True	88.7906	976	1265	95	below_threshold
Marinomonas rhizomae	strain=CECT 7377	GCA_003315485.1	491948	491948	type	True	84.8553	888	1265	95	below_threshold
Marinomonas rhizomae	strain=IVIA-Po-145	GCA_003721275.1	491948	491948	type	True	84.8044	892	1265	95	below_threshold
Marinomonas foliarum	strain=CECT 7731	GCA_003337275.1	491950	491950	type	True	83.4313	758	1265	95	below_threshold
Marinomonas arctica	strain=328	GCA_003259225.1	383750	383750	type	True	82.8513	815	1265	95	below_threshold
Marinomonas alcarazii	strain=CECT 7730	GCA_003208215.1	491949	491949	type	True	82.3932	744	1265	95	below_threshold
Marinomonas shanghaiensis	strain=DSL-35	GCA_003259175.1	2202418	2202418	type	True	82.2581	787	1265	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	81.2752	710	1265	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 23:43:42,109] [INFO] DFAST Taxonomy check result was written to GCA_018820025.1_ASM1882002v1_genomic.fna/tc_result.tsv
[2023-06-18 23:43:42,109] [INFO] ===== Taxonomy check completed =====
[2023-06-18 23:43:42,110] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 23:43:42,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0702213c-6e5f-467d-a0a4-3ccd46670187/dqc_reference/checkm_data
[2023-06-18 23:43:42,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 23:43:42,167] [INFO] Task started: CheckM
[2023-06-18 23:43:42,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018820025.1_ASM1882002v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018820025.1_ASM1882002v1_genomic.fna/checkm_input GCA_018820025.1_ASM1882002v1_genomic.fna/checkm_result
[2023-06-18 23:44:16,055] [INFO] Task succeeded: CheckM
[2023-06-18 23:44:16,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 23:44:16,081] [INFO] ===== Completeness check finished =====
[2023-06-18 23:44:16,081] [INFO] ===== Start GTDB Search =====
[2023-06-18 23:44:16,081] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018820025.1_ASM1882002v1_genomic.fna/markers.fasta)
[2023-06-18 23:44:16,082] [INFO] Task started: Blastn
[2023-06-18 23:44:16,082] [INFO] Running command: blastn -query GCA_018820025.1_ASM1882002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0702213c-6e5f-467d-a0a4-3ccd46670187/dqc_reference/reference_markers_gtdb.fasta -out GCA_018820025.1_ASM1882002v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:44:17,170] [INFO] Task succeeded: Blastn
[2023-06-18 23:44:17,175] [INFO] Selected 7 target genomes.
[2023-06-18 23:44:17,175] [INFO] Target genome list was writen to GCA_018820025.1_ASM1882002v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 23:44:17,180] [INFO] Task started: fastANI
[2023-06-18 23:44:17,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg56cfb723-c53b-416d-bd4e-4a9a0499f989/GCA_018820025.1_ASM1882002v1_genomic.fna.gz --refList GCA_018820025.1_ASM1882002v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018820025.1_ASM1882002v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 23:44:24,450] [INFO] Task succeeded: fastANI
[2023-06-18 23:44:24,461] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 23:44:24,461] [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_900129155.1	s__Marinomonas polaris	97.652	1152	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	conclusive
GCF_000017285.1	s__Marinomonas sp000017285	92.3127	1089	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.39	98.39	0.88	0.88	2	-
GCF_018336955.1	s__Marinomonas sp018336955	88.6448	965	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315485.1	s__Marinomonas rhizomae	84.8462	889	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003337275.1	s__Marinomonas foliarum	83.4333	757	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.18	98.18	0.87	0.87	2	-
GCF_003208215.1	s__Marinomonas alcarazii	82.3932	744	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.70	98.70	0.93	0.93	2	-
GCF_003259175.1	s__Marinomonas shanghaiensis	82.2456	788	1265	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 23:44:24,462] [INFO] GTDB search result was written to GCA_018820025.1_ASM1882002v1_genomic.fna/result_gtdb.tsv
[2023-06-18 23:44:24,463] [INFO] ===== GTDB Search completed =====
[2023-06-18 23:44:24,465] [INFO] DFAST_QC result json was written to GCA_018820025.1_ASM1882002v1_genomic.fna/dqc_result.json
[2023-06-18 23:44:24,466] [INFO] DFAST_QC completed!
[2023-06-18 23:44:24,466] [INFO] Total running time: 0h1m5s