[2024-01-24 14:19:45,305] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:45,307] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:45,307] [INFO] DQC Reference Directory: /var/lib/cwl/stg7547e13c-3215-4869-9fd8-4830acd621a9/dqc_reference
[2024-01-24 14:19:47,130] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:47,131] [INFO] Task started: Prodigal
[2024-01-24 14:19:47,132] [INFO] Running command: gunzip -c /var/lib/cwl/stge083070b-a74f-4919-b7f4-f77358365c03/GCF_000018405.1_ASM1840v1_genomic.fna.gz | prodigal -d GCF_000018405.1_ASM1840v1_genomic.fna/cds.fna -a GCF_000018405.1_ASM1840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:58,306] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:58,307] [INFO] Task started: HMMsearch
[2024-01-24 14:19:58,307] [INFO] Running command: hmmsearch --tblout GCF_000018405.1_ASM1840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7547e13c-3215-4869-9fd8-4830acd621a9/dqc_reference/reference_markers.hmm GCF_000018405.1_ASM1840v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:58,663] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:58,664] [INFO] Found 6/6 markers.
[2024-01-24 14:19:58,693] [INFO] Query marker FASTA was written to GCF_000018405.1_ASM1840v1_genomic.fna/markers.fasta
[2024-01-24 14:19:58,693] [INFO] Task started: Blastn
[2024-01-24 14:19:58,693] [INFO] Running command: blastn -query GCF_000018405.1_ASM1840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7547e13c-3215-4869-9fd8-4830acd621a9/dqc_reference/reference_markers.fasta -out GCF_000018405.1_ASM1840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:59,327] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:59,329] [INFO] Selected 21 target genomes.
[2024-01-24 14:19:59,330] [INFO] Target genome list was writen to GCF_000018405.1_ASM1840v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:59,343] [INFO] Task started: fastANI
[2024-01-24 14:19:59,343] [INFO] Running command: fastANI --query /var/lib/cwl/stge083070b-a74f-4919-b7f4-f77358365c03/GCF_000018405.1_ASM1840v1_genomic.fna.gz --refList GCF_000018405.1_ASM1840v1_genomic.fna/target_genomes.txt --output GCF_000018405.1_ASM1840v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:17,834] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:17,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7547e13c-3215-4869-9fd8-4830acd621a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:17,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7547e13c-3215-4869-9fd8-4830acd621a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:17,842] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:17,842] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:17,842] [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
Desulfosudis oleivorans	strain=Hxd3	GCA_000018405.1	181663	181663	type	True	100.0	1314	1314	95	conclusive
Desulfosarcina alkanivorans	strain=PL12	GCA_009688945.1	571177	571177	type	True	77.1789	142	1314	95	below_threshold
Desulfosarcina ovata subsp. ovata	strain=oXyS1	GCA_009689005.1	2752305	83564	type	True	76.9633	107	1314	95	below_threshold
Desulfosarcina ovata subsp. sediminis	strain=28bB2T	GCA_009688985.1	885957	83564	type	True	76.8489	108	1314	95	below_threshold
Desulfosarcina widdelii	strain=PP31	GCA_009688965.1	947919	947919	type	True	76.6909	137	1314	95	below_threshold
Desulfonema ishimotonii	strain=Tokyo 01	GCA_003851005.1	45657	45657	type	True	76.6378	116	1314	95	below_threshold
Desulfoluna spongiiphila	strain=AA1	GCA_900101345.1	419481	419481	type	True	75.9686	104	1314	95	below_threshold
Desulfospira joergensenii	strain=DSM 10085	GCA_000420085.1	53329	53329	type	True	75.9441	65	1314	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:17,844] [INFO] DFAST Taxonomy check result was written to GCF_000018405.1_ASM1840v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:17,844] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:17,844] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:17,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7547e13c-3215-4869-9fd8-4830acd621a9/dqc_reference/checkm_data
[2024-01-24 14:20:17,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:17,888] [INFO] Task started: CheckM
[2024-01-24 14:20:17,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000018405.1_ASM1840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000018405.1_ASM1840v1_genomic.fna/checkm_input GCF_000018405.1_ASM1840v1_genomic.fna/checkm_result
[2024-01-24 14:20:50,721] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:50,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:50,736] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:50,736] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:50,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000018405.1_ASM1840v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:50,737] [INFO] Task started: Blastn
[2024-01-24 14:20:50,737] [INFO] Running command: blastn -query GCF_000018405.1_ASM1840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7547e13c-3215-4869-9fd8-4830acd621a9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000018405.1_ASM1840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:51,724] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:51,729] [INFO] Selected 23 target genomes.
[2024-01-24 14:20:51,729] [INFO] Target genome list was writen to GCF_000018405.1_ASM1840v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:51,742] [INFO] Task started: fastANI
[2024-01-24 14:20:51,742] [INFO] Running command: fastANI --query /var/lib/cwl/stge083070b-a74f-4919-b7f4-f77358365c03/GCF_000018405.1_ASM1840v1_genomic.fna.gz --refList GCF_000018405.1_ASM1840v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000018405.1_ASM1840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:08,535] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:08,545] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:08,545] [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_000018405.1	s__Desulfosudis oleovorans	100.0	1314	1314	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosudaceae;g__Desulfosudis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900659855.1	s__CR-1 sp900659855	77.0109	76	1314	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__CR-1;g__CR-1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389855.1	s__JAABTD01 sp011389855	76.9007	133	1314	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352605.1	s__Desulfosarcina sp002352605	76.8871	68	1314	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009688965.1	s__Desulfosarcina widdelii	76.7055	136	1314	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390315.1	s__JAABSQ01 sp011390315	76.6409	94	1314	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABSQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390345.1	s__JAABSP01 sp011390345	76.6402	89	1314	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABSP01	95.0	95.08	95.08	0.82	0.82	2	-
GCF_003851005.1	s__Desulfonema_B ishimotonii	76.6378	116	1314	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__Desulfonema_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002085115.1	s__Desulfosudis sp002085115	76.5275	93	1314	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosudaceae;g__Desulfosudis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237405.1	s__Desulfosarcina sp014237405	76.5257	118	1314	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfosarcinaceae;g__Desulfosarcina	95.0	99.69	99.69	0.89	0.89	3	-
GCA_011389555.1	s__Desulfotignum sp011389555	76.3135	75	1314	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390065.1	s__JAABTD01 sp011390065	76.3019	137	1314	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfococcaceae;g__JAABTD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342285.1	s__JAEINQ01 sp016342285	76.2509	131	1314	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__JAEINQ01;g__JAEINQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018829095.1	s__JAHJUF01 sp018829095	76.1829	91	1314	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfatibacillaceae;g__JAHJUF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421285.1	s__Desulfotignum balticum	75.9093	99	1314	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfobacteraceae;g__Desulfotignum	96.875	N/A	N/A	N/A	N/A	1	-
GCA_018822105.1	s__Humidesulfovibrio sp018822105	75.4292	58	1314	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:08,546] [INFO] GTDB search result was written to GCF_000018405.1_ASM1840v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:08,547] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:08,549] [INFO] DFAST_QC result json was written to GCF_000018405.1_ASM1840v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:08,549] [INFO] DFAST_QC completed!
[2024-01-24 14:21:08,550] [INFO] Total running time: 0h1m23s