[2024-01-24 13:12:53,704] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:53,706] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:53,707] [INFO] DQC Reference Directory: /var/lib/cwl/stg904339d0-2ec8-4d86-a4b4-c8d4fa45eb26/dqc_reference
[2024-01-24 13:12:54,986] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:54,987] [INFO] Task started: Prodigal
[2024-01-24 13:12:54,987] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b88985b-2a5d-4666-82a2-e879d571fd34/GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/cds.fna -a GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:06,175] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:06,176] [INFO] Task started: HMMsearch
[2024-01-24 13:13:06,176] [INFO] Running command: hmmsearch --tblout GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg904339d0-2ec8-4d86-a4b4-c8d4fa45eb26/dqc_reference/reference_markers.hmm GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:06,469] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:06,470] [INFO] Found 6/6 markers.
[2024-01-24 13:13:06,504] [INFO] Query marker FASTA was written to GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:13:06,504] [INFO] Task started: Blastn
[2024-01-24 13:13:06,505] [INFO] Running command: blastn -query GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg904339d0-2ec8-4d86-a4b4-c8d4fa45eb26/dqc_reference/reference_markers.fasta -out GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:07,468] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:07,471] [INFO] Selected 16 target genomes.
[2024-01-24 13:13:07,471] [INFO] Target genome list was writen to GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:13:07,485] [INFO] Task started: fastANI
[2024-01-24 13:13:07,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b88985b-2a5d-4666-82a2-e879d571fd34/GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna.gz --refList GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:20,453] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:20,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg904339d0-2ec8-4d86-a4b4-c8d4fa45eb26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:20,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg904339d0-2ec8-4d86-a4b4-c8d4fa45eb26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:20,467] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:20,467] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:20,467] [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
Marinobacter antarcticus	strain=CGMCC 1.10835	GCA_900142385.1	564117	564117	type	True	100.0	1240	1241	95	conclusive
Marinobacter maritimus	strain=CK47	GCA_007671675.1	277961	277961	type	True	84.0566	955	1241	95	below_threshold
Marinobacter aromaticivorans	strain=D15-8P	GCA_002806975.1	1494078	1494078	type	True	81.5356	809	1241	95	below_threshold
Marinobacter salexigens	strain=HJR7	GCA_002806945.1	1925763	1925763	type	True	80.8777	739	1241	95	below_threshold
Marinobacter gelidimuriae	strain=BF04_CF-4	GCA_000372805.1	2739064	2739064	type	True	79.9111	312	1241	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	79.3314	549	1241	95	below_threshold
Marinobacter piscensis	strain=Abdou3	GCA_007671655.1	1562308	1562308	type	True	79.2805	543	1241	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	79.0634	495	1241	95	below_threshold
Marinobacter alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	78.9102	444	1241	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.8365	445	1241	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	78.7782	440	1241	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	78.7544	484	1241	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	78.5542	385	1241	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	77.9033	237	1241	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	77.7984	258	1241	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:20,472] [INFO] DFAST Taxonomy check result was written to GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:13:20,473] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:20,473] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:20,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg904339d0-2ec8-4d86-a4b4-c8d4fa45eb26/dqc_reference/checkm_data
[2024-01-24 13:13:20,478] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:20,523] [INFO] Task started: CheckM
[2024-01-24 13:13:20,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/checkm_input GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:13:57,870] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:57,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:57,886] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:57,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:57,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:13:57,888] [INFO] Task started: Blastn
[2024-01-24 13:13:57,888] [INFO] Running command: blastn -query GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg904339d0-2ec8-4d86-a4b4-c8d4fa45eb26/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:59,261] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:59,264] [INFO] Selected 9 target genomes.
[2024-01-24 13:13:59,264] [INFO] Target genome list was writen to GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:59,276] [INFO] Task started: fastANI
[2024-01-24 13:13:59,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b88985b-2a5d-4666-82a2-e879d571fd34/GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna.gz --refList GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:08,129] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:08,144] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:08,144] [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_900142385.1	s__Marinobacter antarcticus	100.0	1240	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018066865.1	s__Marinobacter sp018066865	84.6432	801	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.94	99.94	0.89	0.89	2	-
GCF_007671675.1	s__Marinobacter maritimus	84.0566	955	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.91	98.91	0.93	0.93	2	-
GCF_900215155.1	s__Marinobacter sp900215155	83.9878	883	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.10	97.17	0.88	0.86	3	-
GCA_011049865.1	s__Marinobacter antarcticus_A	82.6576	803	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407605.1	s__Marinobacter sp002407605	82.5879	861	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001858325.1	s__Marinobacter sp001858325	82.5863	852	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.26	95.26	0.85	0.85	2	-
GCF_003318275.1	s__Marinobacter sp003318275	82.0577	711	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016597815.1	s__Marinobacter sp016597815	81.0477	779	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.88	97.88	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:08,146] [INFO] GTDB search result was written to GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:08,146] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:08,161] [INFO] DFAST_QC result json was written to GCF_900142385.1_IMG-taxon_2667527391_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:14:08,161] [INFO] DFAST_QC completed!
[2024-01-24 13:14:08,161] [INFO] Total running time: 0h1m14s