[2024-01-24 15:02:07,440] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:07,443] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:07,444] [INFO] DQC Reference Directory: /var/lib/cwl/stgca768f19-d1d1-4c80-a56a-e492c96d46a5/dqc_reference
[2024-01-24 15:02:09,599] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:09,600] [INFO] Task started: Prodigal
[2024-01-24 15:02:09,601] [INFO] Running command: gunzip -c /var/lib/cwl/stg76a1b0e2-3840-4f3c-9688-ab8ce19b0c8b/GCF_004339665.1_ASM433966v1_genomic.fna.gz | prodigal -d GCF_004339665.1_ASM433966v1_genomic.fna/cds.fna -a GCF_004339665.1_ASM433966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:22,936] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:22,937] [INFO] Task started: HMMsearch
[2024-01-24 15:02:22,937] [INFO] Running command: hmmsearch --tblout GCF_004339665.1_ASM433966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca768f19-d1d1-4c80-a56a-e492c96d46a5/dqc_reference/reference_markers.hmm GCF_004339665.1_ASM433966v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:23,228] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:23,229] [INFO] Found 6/6 markers.
[2024-01-24 15:02:23,278] [INFO] Query marker FASTA was written to GCF_004339665.1_ASM433966v1_genomic.fna/markers.fasta
[2024-01-24 15:02:23,279] [INFO] Task started: Blastn
[2024-01-24 15:02:23,279] [INFO] Running command: blastn -query GCF_004339665.1_ASM433966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca768f19-d1d1-4c80-a56a-e492c96d46a5/dqc_reference/reference_markers.fasta -out GCF_004339665.1_ASM433966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:24,284] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:24,287] [INFO] Selected 17 target genomes.
[2024-01-24 15:02:24,288] [INFO] Target genome list was writen to GCF_004339665.1_ASM433966v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:24,306] [INFO] Task started: fastANI
[2024-01-24 15:02:24,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg76a1b0e2-3840-4f3c-9688-ab8ce19b0c8b/GCF_004339665.1_ASM433966v1_genomic.fna.gz --refList GCF_004339665.1_ASM433966v1_genomic.fna/target_genomes.txt --output GCF_004339665.1_ASM433966v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:42,716] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:42,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca768f19-d1d1-4c80-a56a-e492c96d46a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:42,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca768f19-d1d1-4c80-a56a-e492c96d46a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:42,730] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:02:42,731] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:42,731] [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
Azotobacter chroococcum	strain=DSM 2286	GCA_004339665.1	353	353	type	True	100.0	1570	1572	95	conclusive
Azotobacter chroococcum	strain=ATCC 9043	GCA_004327905.1	353	353	type	True	99.9974	1572	1572	95	conclusive
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	96.1346	1364	1572	95	conclusive
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	91.2517	1165	1572	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	83.8263	818	1572	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	83.7457	788	1572	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.1537	756	1572	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	82.8836	788	1572	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	82.8411	702	1572	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	82.327	738	1572	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_000802425.1	706570	706570	type	True	82.2054	660	1572	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	82.149	667	1572	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.0423	742	1572	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	81.8983	791	1572	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	81.8534	694	1572	95	below_threshold
Pseudomonas indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	81.8316	789	1572	95	below_threshold
Pseudomonas sediminis	strain=PI11	GCA_002741105.1	1691904	1691904	type	True	80.7375	677	1572	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:42,732] [INFO] DFAST Taxonomy check result was written to GCF_004339665.1_ASM433966v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:42,733] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:42,733] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:42,733] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca768f19-d1d1-4c80-a56a-e492c96d46a5/dqc_reference/checkm_data
[2024-01-24 15:02:42,734] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:42,782] [INFO] Task started: CheckM
[2024-01-24 15:02:42,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004339665.1_ASM433966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004339665.1_ASM433966v1_genomic.fna/checkm_input GCF_004339665.1_ASM433966v1_genomic.fna/checkm_result
[2024-01-24 15:03:25,049] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:25,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:25,070] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:25,070] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:25,071] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004339665.1_ASM433966v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:25,071] [INFO] Task started: Blastn
[2024-01-24 15:03:25,071] [INFO] Running command: blastn -query GCF_004339665.1_ASM433966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca768f19-d1d1-4c80-a56a-e492c96d46a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_004339665.1_ASM433966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:27,068] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:27,076] [INFO] Selected 19 target genomes.
[2024-01-24 15:03:27,077] [INFO] Target genome list was writen to GCF_004339665.1_ASM433966v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:27,098] [INFO] Task started: fastANI
[2024-01-24 15:03:27,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg76a1b0e2-3840-4f3c-9688-ab8ce19b0c8b/GCF_004339665.1_ASM433966v1_genomic.fna.gz --refList GCF_004339665.1_ASM433966v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004339665.1_ASM433966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:49,683] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:49,699] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:49,699] [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_004339665.1	s__Azotobacter chroococcum	100.0	1570	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.27	96.18	0.89	0.83	10	conclusive
GCF_009363155.1	s__Azotobacter salinestris	91.4578	1312	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110885.1	s__Azotobacter beijerinckii	91.2597	1164	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.34	96.47	0.86	0.85	5	-
GCF_000380335.1	s__Azotobacter vinelandii	89.4322	1210	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	99.84	99.43	0.98	0.95	5	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	84.0154	762	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_900115715.1	s__Pseudomonas_K sagittaria	83.8736	809	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104805.1	s__Pseudomonas_K oryzae	83.8013	822	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105885.1	s__Pseudomonas_K guangdongensis	83.6753	688	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.99	98.99	0.99	0.99	2	-
GCF_003205495.1	s__Pseudomonas_E alcaligenes_B	83.3639	726	1572	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_018398425.1	s__Pseudomonas_E lalucatii	83.1339	757	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.68	99.28	0.97	0.92	4	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	82.9504	781	1572	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_000364625.1	s__Pseudomonas_E thermotolerans	82.8597	701	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.25	99.24	0.93	0.93	3	-
GCF_007109405.1	s__VJOY01 sp007109405	81.8854	691	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__VJOY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002091635.1	s__Pseudomonas_M indica	81.8597	784	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	99.16	98.73	0.94	0.91	4	-
GCF_007993865.1	s__Pseudomonas_E sp007993865	80.6877	631	1572	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_003331055.1	s__Pseudomonas_E sp003331055	80.3689	647	1572	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_013386165.1	s__Pseudomonas_E gingeri_C	79.5203	601	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	98.31	0.93	0.92	4	-
GCF_001186335.1	s__Pseudomonas_E trivialis_B	78.7866	535	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.34	95.31	0.86	0.86	8	-
GCF_009834515.1	s__Pseudomonas_E sp009834515	78.6164	517	1572	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:49,701] [INFO] GTDB search result was written to GCF_004339665.1_ASM433966v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:49,702] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:49,706] [INFO] DFAST_QC result json was written to GCF_004339665.1_ASM433966v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:49,706] [INFO] DFAST_QC completed!
[2024-01-24 15:03:49,706] [INFO] Total running time: 0h1m42s