[2024-01-24 11:26:37,814] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:37,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:37,816] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c9979c7-1b57-4432-b756-618491b5e80f/dqc_reference
[2024-01-24 11:26:39,086] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:39,087] [INFO] Task started: Prodigal
[2024-01-24 11:26:39,087] [INFO] Running command: gunzip -c /var/lib/cwl/stg8dfdedac-9322-428f-a6e9-c4d0646d8333/GCF_004799025.1_ASM479902v1_genomic.fna.gz | prodigal -d GCF_004799025.1_ASM479902v1_genomic.fna/cds.fna -a GCF_004799025.1_ASM479902v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:54,735] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:54,735] [INFO] Task started: HMMsearch
[2024-01-24 11:26:54,736] [INFO] Running command: hmmsearch --tblout GCF_004799025.1_ASM479902v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c9979c7-1b57-4432-b756-618491b5e80f/dqc_reference/reference_markers.hmm GCF_004799025.1_ASM479902v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:55,043] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:55,045] [INFO] Found 6/6 markers.
[2024-01-24 11:26:55,094] [INFO] Query marker FASTA was written to GCF_004799025.1_ASM479902v1_genomic.fna/markers.fasta
[2024-01-24 11:26:55,095] [INFO] Task started: Blastn
[2024-01-24 11:26:55,095] [INFO] Running command: blastn -query GCF_004799025.1_ASM479902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c9979c7-1b57-4432-b756-618491b5e80f/dqc_reference/reference_markers.fasta -out GCF_004799025.1_ASM479902v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:56,047] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:56,051] [INFO] Selected 17 target genomes.
[2024-01-24 11:26:56,051] [INFO] Target genome list was writen to GCF_004799025.1_ASM479902v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:56,074] [INFO] Task started: fastANI
[2024-01-24 11:26:56,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dfdedac-9322-428f-a6e9-c4d0646d8333/GCF_004799025.1_ASM479902v1_genomic.fna.gz --refList GCF_004799025.1_ASM479902v1_genomic.fna/target_genomes.txt --output GCF_004799025.1_ASM479902v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:11,367] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:11,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c9979c7-1b57-4432-b756-618491b5e80f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:11,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c9979c7-1b57-4432-b756-618491b5e80f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:11,381] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:27:11,381] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:11,381] [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
Panacagrimonas perspica	strain=DSM 26377	GCA_004799025.1	381431	381431	type	True	100.0	1757	1763	95	conclusive
Panacagrimonas perspica	strain=DSM 26377	GCA_004364935.1	381431	381431	type	True	99.9953	1757	1763	95	conclusive
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	78.8104	516	1763	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	78.7636	511	1763	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	78.6908	506	1763	95	below_threshold
Hydrocarboniphaga daqingensis	strain=CGMCC 1.7049	GCA_900129825.1	490188	490188	type	True	78.6189	426	1763	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	78.6056	532	1763	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	78.6002	533	1763	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	78.2254	429	1763	95	below_threshold
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	77.6137	241	1763	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.5963	195	1763	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	76.547	162	1763	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.4529	200	1763	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	76.4178	226	1763	95	below_threshold
Pseudomonas mangrovi	strain=TC11	GCA_003052585.1	2161748	2161748	type	True	76.4019	143	1763	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.2237	197	1763	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	75.9408	124	1763	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:11,383] [INFO] DFAST Taxonomy check result was written to GCF_004799025.1_ASM479902v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:11,384] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:11,384] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:11,384] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c9979c7-1b57-4432-b756-618491b5e80f/dqc_reference/checkm_data
[2024-01-24 11:27:11,385] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:11,437] [INFO] Task started: CheckM
[2024-01-24 11:27:11,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004799025.1_ASM479902v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004799025.1_ASM479902v1_genomic.fna/checkm_input GCF_004799025.1_ASM479902v1_genomic.fna/checkm_result
[2024-01-24 11:28:04,962] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:04,963] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:04,987] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:04,987] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:04,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004799025.1_ASM479902v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:04,988] [INFO] Task started: Blastn
[2024-01-24 11:28:04,988] [INFO] Running command: blastn -query GCF_004799025.1_ASM479902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c9979c7-1b57-4432-b756-618491b5e80f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004799025.1_ASM479902v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:06,812] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:06,817] [INFO] Selected 16 target genomes.
[2024-01-24 11:28:06,817] [INFO] Target genome list was writen to GCF_004799025.1_ASM479902v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:06,831] [INFO] Task started: fastANI
[2024-01-24 11:28:06,831] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dfdedac-9322-428f-a6e9-c4d0646d8333/GCF_004799025.1_ASM479902v1_genomic.fna.gz --refList GCF_004799025.1_ASM479902v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004799025.1_ASM479902v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:21,031] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:21,049] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:21,049] [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_004364935.1	s__Panacagrimonas perspica	99.9953	1757	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Panacagrimonas	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002930645.1	s__Solimonas_A fluminis	78.8455	511	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428335.1	s__Solimonas_A sp003428335	78.7562	551	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474945.1	s__Solimonas soli	78.7554	512	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201205.1	s__Sinimarinibacterium flocculans	78.6761	472	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382285.1	s__Solimonas variicoloris	78.6692	509	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCA_008012115.1	s__Stenotrophobium sp008012115	78.6368	419	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129825.1	s__Hydrocarboniphaga daqingensis	78.6226	425	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000271305.1	s__Hydrocarboniphaga effusa	78.6081	533	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426685.1	s__Solimonas flava	78.5993	533	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCA_016182805.1	s__JACPFV01 sp016182805	78.5063	276	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__JACPFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111015.1	s__Solimonas aquatica	78.1927	434	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779605.1	s__Nevskia sp016779605	78.1726	425	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003052585.1	s__Pseudomonas_E mangrovi	76.3881	144	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000327045.1	s__Thioflavicoccus mobilis	75.9406	124	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thioflavicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790695.1	s__JAEUOS01 sp016790695	75.8391	252	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__JAEUOS01;g__JAEUOS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:21,051] [INFO] GTDB search result was written to GCF_004799025.1_ASM479902v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:21,051] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:21,055] [INFO] DFAST_QC result json was written to GCF_004799025.1_ASM479902v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:21,055] [INFO] DFAST_QC completed!
[2024-01-24 11:28:21,055] [INFO] Total running time: 0h1m43s