[2023-06-08 07:43:26,038] [INFO] DFAST_QC pipeline started.
[2023-06-08 07:43:26,045] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 07:43:26,045] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7c0c54f-611a-49b0-8302-e115cd391eba/dqc_reference
[2023-06-08 07:43:27,489] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 07:43:27,490] [INFO] Task started: Prodigal
[2023-06-08 07:43:27,490] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b57fdcc-d926-4d1e-872b-a2a01ea6bcde/GCA_945897375.1_MoE-23oct19-335_genomic.fna.gz | prodigal -d GCA_945897375.1_MoE-23oct19-335_genomic.fna/cds.fna -a GCA_945897375.1_MoE-23oct19-335_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 07:44:00,779] [INFO] Task succeeded: Prodigal
[2023-06-08 07:44:00,780] [INFO] Task started: HMMsearch
[2023-06-08 07:44:00,780] [INFO] Running command: hmmsearch --tblout GCA_945897375.1_MoE-23oct19-335_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7c0c54f-611a-49b0-8302-e115cd391eba/dqc_reference/reference_markers.hmm GCA_945897375.1_MoE-23oct19-335_genomic.fna/protein.faa > /dev/null
[2023-06-08 07:44:01,069] [INFO] Task succeeded: HMMsearch
[2023-06-08 07:44:01,070] [INFO] Found 6/6 markers.
[2023-06-08 07:44:01,114] [INFO] Query marker FASTA was written to GCA_945897375.1_MoE-23oct19-335_genomic.fna/markers.fasta
[2023-06-08 07:44:01,114] [INFO] Task started: Blastn
[2023-06-08 07:44:01,115] [INFO] Running command: blastn -query GCA_945897375.1_MoE-23oct19-335_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7c0c54f-611a-49b0-8302-e115cd391eba/dqc_reference/reference_markers.fasta -out GCA_945897375.1_MoE-23oct19-335_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:44:01,707] [INFO] Task succeeded: Blastn
[2023-06-08 07:44:01,711] [INFO] Selected 23 target genomes.
[2023-06-08 07:44:01,711] [INFO] Target genome list was writen to GCA_945897375.1_MoE-23oct19-335_genomic.fna/target_genomes.txt
[2023-06-08 07:44:01,715] [INFO] Task started: fastANI
[2023-06-08 07:44:01,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b57fdcc-d926-4d1e-872b-a2a01ea6bcde/GCA_945897375.1_MoE-23oct19-335_genomic.fna.gz --refList GCA_945897375.1_MoE-23oct19-335_genomic.fna/target_genomes.txt --output GCA_945897375.1_MoE-23oct19-335_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 07:44:19,567] [INFO] Task succeeded: fastANI
[2023-06-08 07:44:19,568] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7c0c54f-611a-49b0-8302-e115cd391eba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 07:44:19,569] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7c0c54f-611a-49b0-8302-e115cd391eba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 07:44:19,581] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 07:44:19,582] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 07:44:19,582] [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
Prosthecobacter vanneervenii	strain=DSM 12252	GCA_014203095.1	48466	48466	type	True	79.265	740	1491	95	below_threshold
Brevifollis gellanilyticus	strain=NBRC 108608	GCA_007992435.1	748831	748831	type	True	77.7868	453	1491	95	below_threshold
Prosthecobacter debontii	strain=ATCC 700200	GCA_900167535.1	48467	48467	type	True	77.3315	218	1491	95	below_threshold
Prosthecobacter fusiformis	strain=ATCC 25309	GCA_004364345.1	48464	48464	type	True	77.229	222	1491	95	below_threshold
Prosthecobacter dejongeii	strain=DSM 12251	GCA_014203045.1	48465	48465	type	True	77.0763	225	1491	95	below_threshold
Phragmitibacter flavus	strain=MG-N-17	GCA_005780165.1	2576071	2576071	type	True	76.9107	109	1491	95	below_threshold
Verrucomicrobium spinosum	strain=DSM 4136	GCA_000172155.1	2736	2736	type	True	76.5906	152	1491	95	below_threshold
Verrucomicrobium spinosum	strain=JCM 18804	GCA_001313125.1	2736	2736	type	True	76.583	146	1491	95	below_threshold
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.2175	100	1491	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 07:44:19,588] [INFO] DFAST Taxonomy check result was written to GCA_945897375.1_MoE-23oct19-335_genomic.fna/tc_result.tsv
[2023-06-08 07:44:19,589] [INFO] ===== Taxonomy check completed =====
[2023-06-08 07:44:19,589] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 07:44:19,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7c0c54f-611a-49b0-8302-e115cd391eba/dqc_reference/checkm_data
[2023-06-08 07:44:19,591] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 07:44:19,641] [INFO] Task started: CheckM
[2023-06-08 07:44:19,641] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945897375.1_MoE-23oct19-335_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945897375.1_MoE-23oct19-335_genomic.fna/checkm_input GCA_945897375.1_MoE-23oct19-335_genomic.fna/checkm_result
[2023-06-08 07:45:48,934] [INFO] Task succeeded: CheckM
[2023-06-08 07:45:48,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 07:45:48,975] [INFO] ===== Completeness check finished =====
[2023-06-08 07:45:48,976] [INFO] ===== Start GTDB Search =====
[2023-06-08 07:45:48,976] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945897375.1_MoE-23oct19-335_genomic.fna/markers.fasta)
[2023-06-08 07:45:48,976] [INFO] Task started: Blastn
[2023-06-08 07:45:48,976] [INFO] Running command: blastn -query GCA_945897375.1_MoE-23oct19-335_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7c0c54f-611a-49b0-8302-e115cd391eba/dqc_reference/reference_markers_gtdb.fasta -out GCA_945897375.1_MoE-23oct19-335_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 07:45:49,791] [INFO] Task succeeded: Blastn
[2023-06-08 07:45:49,797] [INFO] Selected 12 target genomes.
[2023-06-08 07:45:49,797] [INFO] Target genome list was writen to GCA_945897375.1_MoE-23oct19-335_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 07:45:49,801] [INFO] Task started: fastANI
[2023-06-08 07:45:49,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b57fdcc-d926-4d1e-872b-a2a01ea6bcde/GCA_945897375.1_MoE-23oct19-335_genomic.fna.gz --refList GCA_945897375.1_MoE-23oct19-335_genomic.fna/target_genomes_gtdb.txt --output GCA_945897375.1_MoE-23oct19-335_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 07:46:05,014] [INFO] Task succeeded: fastANI
[2023-06-08 07:46:05,026] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 07:46:05,027] [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
GCA_003506995.1	s__Prosthecobacter sp003506995	86.115	930	1491	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879935.1	s__Prosthecobacter sp014879935	81.695	941	1491	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795375.1	s__Prosthecobacter sp016795375	81.0664	754	1491	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075365.1	s__Prosthecobacter sp015075365	80.8423	777	1491	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795465.1	s__Prosthecobacter sp016795465	80.6015	753	1491	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903848465.1	s__Prosthecobacter sp903848465	80.2946	764	1491	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	99.97	99.92	0.97	0.96	6	-
GCA_903838675.1	s__Prosthecobacter sp903838675	80.0481	803	1491	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	99.92	99.91	0.96	0.96	3	-
GCA_002482965.1	s__Prosthecobacter sp002482965	79.9829	794	1491	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279765.1	s__Prosthecobacter sp002279765	79.9791	799	1491	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017301975.1	s__Prosthecobacter sp017301975	79.8711	797	1491	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336895.1	s__Prosthecobacter sp002336895	79.292	771	1491	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203095.1	s__Prosthecobacter vanneervenii	79.2537	741	1491	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 07:46:05,029] [INFO] GTDB search result was written to GCA_945897375.1_MoE-23oct19-335_genomic.fna/result_gtdb.tsv
[2023-06-08 07:46:05,029] [INFO] ===== GTDB Search completed =====
[2023-06-08 07:46:05,047] [INFO] DFAST_QC result json was written to GCA_945897375.1_MoE-23oct19-335_genomic.fna/dqc_result.json
[2023-06-08 07:46:05,047] [INFO] DFAST_QC completed!
[2023-06-08 07:46:05,048] [INFO] Total running time: 0h2m39s