[2024-01-24 13:31:42,530] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:42,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:42,536] [INFO] DQC Reference Directory: /var/lib/cwl/stg4042cd8e-7b83-4b5b-97e8-f5d91da796c5/dqc_reference
[2024-01-24 13:31:43,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:43,870] [INFO] Task started: Prodigal
[2024-01-24 13:31:43,871] [INFO] Running command: gunzip -c /var/lib/cwl/stg865fe79f-ab42-42c1-8cb9-3becfaffdcb0/GCF_003996985.1_ASM399698v1_genomic.fna.gz | prodigal -d GCF_003996985.1_ASM399698v1_genomic.fna/cds.fna -a GCF_003996985.1_ASM399698v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:59,471] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:59,472] [INFO] Task started: HMMsearch
[2024-01-24 13:31:59,472] [INFO] Running command: hmmsearch --tblout GCF_003996985.1_ASM399698v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4042cd8e-7b83-4b5b-97e8-f5d91da796c5/dqc_reference/reference_markers.hmm GCF_003996985.1_ASM399698v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:59,779] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:59,781] [INFO] Found 6/6 markers.
[2024-01-24 13:31:59,820] [INFO] Query marker FASTA was written to GCF_003996985.1_ASM399698v1_genomic.fna/markers.fasta
[2024-01-24 13:31:59,820] [INFO] Task started: Blastn
[2024-01-24 13:31:59,821] [INFO] Running command: blastn -query GCF_003996985.1_ASM399698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4042cd8e-7b83-4b5b-97e8-f5d91da796c5/dqc_reference/reference_markers.fasta -out GCF_003996985.1_ASM399698v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:00,428] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:00,432] [INFO] Selected 22 target genomes.
[2024-01-24 13:32:00,432] [INFO] Target genome list was writen to GCF_003996985.1_ASM399698v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:00,443] [INFO] Task started: fastANI
[2024-01-24 13:32:00,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg865fe79f-ab42-42c1-8cb9-3becfaffdcb0/GCF_003996985.1_ASM399698v1_genomic.fna.gz --refList GCF_003996985.1_ASM399698v1_genomic.fna/target_genomes.txt --output GCF_003996985.1_ASM399698v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:17,884] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:17,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4042cd8e-7b83-4b5b-97e8-f5d91da796c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:17,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4042cd8e-7b83-4b5b-97e8-f5d91da796c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:17,893] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:17,893] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:17,894] [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
Ancylomarina longa	strain=T3-2 S1-C	GCA_003996985.1	2487017	2487017	type	True	100.0	1292	1295	95	conclusive
Marinifilum fragile	strain=JCM 15579	GCA_001310955.1	570161	570161	type	True	78.0509	332	1295	95	below_threshold
Ancylomarina salipaludis	strain=SHSM-M15	GCA_004122035.1	2501299	2501299	type	True	77.9659	158	1295	95	below_threshold
Marinifilum breve	strain=JC075	GCA_003202155.1	2184082	2184082	type	True	77.8764	362	1295	95	below_threshold
Marinifilum flexuosum	strain=DSM 21950	GCA_003610555.1	1117708	1117708	type	True	77.8284	360	1295	95	below_threshold
Labilibaculum filiforme	strain=59.16B	GCA_002843315.1	1940526	1940526	type	True	77.8243	375	1295	95	below_threshold
Labilibaculum antarcticum	strain=SPP2	GCA_002356295.1	1717717	1717717	type	True	77.7697	391	1295	95	below_threshold
Labilibaculum manganireducens	strain=59.10-2M	GCA_002843385.1	1940525	1940525	type	True	77.7214	403	1295	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:17,896] [INFO] DFAST Taxonomy check result was written to GCF_003996985.1_ASM399698v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:17,897] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:17,897] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:17,898] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4042cd8e-7b83-4b5b-97e8-f5d91da796c5/dqc_reference/checkm_data
[2024-01-24 13:32:17,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:17,952] [INFO] Task started: CheckM
[2024-01-24 13:32:17,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003996985.1_ASM399698v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003996985.1_ASM399698v1_genomic.fna/checkm_input GCF_003996985.1_ASM399698v1_genomic.fna/checkm_result
[2024-01-24 13:33:07,177] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:07,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.86%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:07,207] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:07,207] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:07,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003996985.1_ASM399698v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:07,208] [INFO] Task started: Blastn
[2024-01-24 13:33:07,208] [INFO] Running command: blastn -query GCF_003996985.1_ASM399698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4042cd8e-7b83-4b5b-97e8-f5d91da796c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003996985.1_ASM399698v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:08,034] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:08,038] [INFO] Selected 19 target genomes.
[2024-01-24 13:33:08,038] [INFO] Target genome list was writen to GCF_003996985.1_ASM399698v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:08,073] [INFO] Task started: fastANI
[2024-01-24 13:33:08,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg865fe79f-ab42-42c1-8cb9-3becfaffdcb0/GCF_003996985.1_ASM399698v1_genomic.fna.gz --refList GCF_003996985.1_ASM399698v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003996985.1_ASM399698v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:22,551] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:22,568] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:22,568] [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_003996985.1	s__Ancylomarina_A longa	100.0	1292	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009295825.1	s__Marinifilum sp009295825	78.0472	411	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342745.1	s__Labilibaculum sp016342745	78.0234	354	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936255.1	s__Labilibaculum sp016936255	77.8913	380	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202155.1	s__Marinifilum breve	77.8761	362	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009795715.1	s__Labilibaculum euxinus	77.857	408	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	97.85	97.85	0.89	0.89	3	-
GCF_002843315.1	s__Labilibaculum filiforme	77.831	375	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610555.1	s__Marinifilum flexuosum	77.8188	361	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Marinifilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356295.1	s__Labilibaculum antarcticum	77.7697	391	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002843385.1	s__Labilibaculum manganireducens	77.7297	402	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016760525.1	s__Labilibaculum sp016760525	77.655	207	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Labilibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003863355.1	s__Ancylomarina euxinus	77.6188	161	1295	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinifilaceae;g__Ancylomarina	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:22,570] [INFO] GTDB search result was written to GCF_003996985.1_ASM399698v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:22,571] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:22,574] [INFO] DFAST_QC result json was written to GCF_003996985.1_ASM399698v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:22,574] [INFO] DFAST_QC completed!
[2024-01-24 13:33:22,574] [INFO] Total running time: 0h1m40s