[2024-01-24 13:01:38,047] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:38,049] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:38,049] [INFO] DQC Reference Directory: /var/lib/cwl/stg783ea099-7720-4923-80b6-fa0c1248f663/dqc_reference
[2024-01-24 13:01:40,904] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:40,905] [INFO] Task started: Prodigal
[2024-01-24 13:01:40,906] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f3dac86-c660-4790-82fa-e00ca02491cb/GCF_007671655.1_ASM767165v1_genomic.fna.gz | prodigal -d GCF_007671655.1_ASM767165v1_genomic.fna/cds.fna -a GCF_007671655.1_ASM767165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:50,921] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:50,922] [INFO] Task started: HMMsearch
[2024-01-24 13:01:50,922] [INFO] Running command: hmmsearch --tblout GCF_007671655.1_ASM767165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg783ea099-7720-4923-80b6-fa0c1248f663/dqc_reference/reference_markers.hmm GCF_007671655.1_ASM767165v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:51,230] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:51,231] [INFO] Found 6/6 markers.
[2024-01-24 13:01:51,269] [INFO] Query marker FASTA was written to GCF_007671655.1_ASM767165v1_genomic.fna/markers.fasta
[2024-01-24 13:01:51,270] [INFO] Task started: Blastn
[2024-01-24 13:01:51,270] [INFO] Running command: blastn -query GCF_007671655.1_ASM767165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg783ea099-7720-4923-80b6-fa0c1248f663/dqc_reference/reference_markers.fasta -out GCF_007671655.1_ASM767165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:52,107] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:52,111] [INFO] Selected 18 target genomes.
[2024-01-24 13:01:52,111] [INFO] Target genome list was writen to GCF_007671655.1_ASM767165v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:52,118] [INFO] Task started: fastANI
[2024-01-24 13:01:52,118] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f3dac86-c660-4790-82fa-e00ca02491cb/GCF_007671655.1_ASM767165v1_genomic.fna.gz --refList GCF_007671655.1_ASM767165v1_genomic.fna/target_genomes.txt --output GCF_007671655.1_ASM767165v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:07,828] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:07,829] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg783ea099-7720-4923-80b6-fa0c1248f663/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:07,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg783ea099-7720-4923-80b6-fa0c1248f663/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:07,842] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:07,843] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:07,843] [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 piscensis	strain=Abdou3	GCA_007671655.1	1562308	1562308	type	True	100.0	1108	1108	95	conclusive
Marinobacter aromaticivorans	strain=D15-8P	GCA_002806975.1	1494078	1494078	type	True	79.8777	586	1108	95	below_threshold
Marinobacter salexigens	strain=HJR7	GCA_002806945.1	1925763	1925763	type	True	79.8482	559	1108	95	below_threshold
Marinobacter maritimus	strain=CK47	GCA_007671675.1	277961	277961	type	True	79.2905	559	1108	95	below_threshold
Marinobacter antarcticus	strain=CGMCC 1.10835	GCA_900142385.1	564117	564117	type	True	79.2759	557	1108	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	78.734	354	1108	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.4362	313	1108	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	78.4303	313	1108	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	78.3968	365	1108	95	below_threshold
Marinobacter alexandrii	strain=LZ-8	GCA_005871205.1	2570351	2570351	type	True	78.3563	315	1108	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	78.3388	225	1108	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	78.2631	322	1108	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	78.1343	347	1108	95	below_threshold
Marinobacter nitratireducens	strain=AK21	GCA_000708045.1	1137280	1137280	type	True	78.1169	297	1108	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:07,847] [INFO] DFAST Taxonomy check result was written to GCF_007671655.1_ASM767165v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:07,847] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:07,848] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:07,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg783ea099-7720-4923-80b6-fa0c1248f663/dqc_reference/checkm_data
[2024-01-24 13:02:07,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:07,895] [INFO] Task started: CheckM
[2024-01-24 13:02:07,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007671655.1_ASM767165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007671655.1_ASM767165v1_genomic.fna/checkm_input GCF_007671655.1_ASM767165v1_genomic.fna/checkm_result
[2024-01-24 13:02:43,243] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:43,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:43,268] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:43,269] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:43,270] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007671655.1_ASM767165v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:43,270] [INFO] Task started: Blastn
[2024-01-24 13:02:43,270] [INFO] Running command: blastn -query GCF_007671655.1_ASM767165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg783ea099-7720-4923-80b6-fa0c1248f663/dqc_reference/reference_markers_gtdb.fasta -out GCF_007671655.1_ASM767165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:44,522] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:44,527] [INFO] Selected 16 target genomes.
[2024-01-24 13:02:44,527] [INFO] Target genome list was writen to GCF_007671655.1_ASM767165v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:44,555] [INFO] Task started: fastANI
[2024-01-24 13:02:44,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f3dac86-c660-4790-82fa-e00ca02491cb/GCF_007671655.1_ASM767165v1_genomic.fna.gz --refList GCF_007671655.1_ASM767165v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007671655.1_ASM767165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:56,444] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:56,459] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:56,460] [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_007671655.1	s__Marinobacter piscensis	100.0	1108	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.90	96.90	0.91	0.91	2	conclusive
GCF_002806975.1	s__Marinobacter aromaticivorans	79.8541	589	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002806945.1	s__Marinobacter salexigens	79.8429	560	1108	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	79.3798	518	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.88	97.88	0.89	0.89	2	-
GCF_900142385.1	s__Marinobacter antarcticus	79.2963	554	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007671675.1	s__Marinobacter maritimus	79.2906	559	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.91	98.91	0.93	0.93	2	-
GCA_018066865.1	s__Marinobacter sp018066865	79.1558	480	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.94	99.94	0.89	0.89	2	-
GCF_016597725.1	s__Marinobacter sp016597725	79.0842	480	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318275.1	s__Marinobacter sp003318275	78.8408	388	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258215.1	s__Marinobacter vinifirmus	78.7369	352	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCA_011049865.1	s__Marinobacter antarcticus_A	78.6911	433	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	78.5637	327	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188435.1	s__Marinobacter sp900188435	78.4066	338	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005871205.1	s__Marinobacter alexandrii	78.356	315	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.69	98.69	0.90	0.90	2	-
GCF_003994855.1	s__Marinobacter sp003994855	78.3552	321	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708045.1	s__Marinobacter nitratireducens	78.1079	297	1108	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.86	98.83	0.90	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:56,462] [INFO] GTDB search result was written to GCF_007671655.1_ASM767165v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:56,462] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:56,466] [INFO] DFAST_QC result json was written to GCF_007671655.1_ASM767165v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:56,466] [INFO] DFAST_QC completed!
[2024-01-24 13:02:56,466] [INFO] Total running time: 0h1m18s