[2024-01-24 13:40:34,090] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,094] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,094] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb062313-32a4-4e7f-9783-8d275d6748da/dqc_reference
[2024-01-24 13:40:35,388] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:35,389] [INFO] Task started: Prodigal
[2024-01-24 13:40:35,389] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c0cc86b-a0f6-4ac8-bc3c-0495254b5369/GCF_004358695.1_ASM435869v1_genomic.fna.gz | prodigal -d GCF_004358695.1_ASM435869v1_genomic.fna/cds.fna -a GCF_004358695.1_ASM435869v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:45,005] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:45,005] [INFO] Task started: HMMsearch
[2024-01-24 13:40:45,005] [INFO] Running command: hmmsearch --tblout GCF_004358695.1_ASM435869v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb062313-32a4-4e7f-9783-8d275d6748da/dqc_reference/reference_markers.hmm GCF_004358695.1_ASM435869v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:45,305] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:45,306] [INFO] Found 6/6 markers.
[2024-01-24 13:40:45,349] [INFO] Query marker FASTA was written to GCF_004358695.1_ASM435869v1_genomic.fna/markers.fasta
[2024-01-24 13:40:45,350] [INFO] Task started: Blastn
[2024-01-24 13:40:45,350] [INFO] Running command: blastn -query GCF_004358695.1_ASM435869v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb062313-32a4-4e7f-9783-8d275d6748da/dqc_reference/reference_markers.fasta -out GCF_004358695.1_ASM435869v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:46,395] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:46,398] [INFO] Selected 23 target genomes.
[2024-01-24 13:40:46,399] [INFO] Target genome list was writen to GCF_004358695.1_ASM435869v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:46,409] [INFO] Task started: fastANI
[2024-01-24 13:40:46,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c0cc86b-a0f6-4ac8-bc3c-0495254b5369/GCF_004358695.1_ASM435869v1_genomic.fna.gz --refList GCF_004358695.1_ASM435869v1_genomic.fna/target_genomes.txt --output GCF_004358695.1_ASM435869v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:08,094] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:08,094] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb062313-32a4-4e7f-9783-8d275d6748da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:08,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb062313-32a4-4e7f-9783-8d275d6748da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:08,113] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:08,113] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:08,113] [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
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	100.0	1102	1104	95	conclusive
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	79.7561	558	1104	95	below_threshold
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	79.5873	559	1104	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	79.5077	489	1104	95	below_threshold
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	79.5009	510	1104	95	below_threshold
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	79.4865	506	1104	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.7286	434	1104	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.7085	484	1104	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.6547	431	1104	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.6483	448	1104	95	below_threshold
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	78.6309	424	1104	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	78.6197	425	1104	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.6177	437	1104	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	78.3901	388	1104	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	78.2617	423	1104	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.2417	425	1104	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.1767	379	1104	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	78.15	422	1104	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.1073	437	1104	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.0496	468	1104	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	78.0435	439	1104	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.897	434	1104	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.8577	365	1104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:08,115] [INFO] DFAST Taxonomy check result was written to GCF_004358695.1_ASM435869v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:08,116] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:08,116] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:08,116] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb062313-32a4-4e7f-9783-8d275d6748da/dqc_reference/checkm_data
[2024-01-24 13:41:08,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:08,160] [INFO] Task started: CheckM
[2024-01-24 13:41:08,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004358695.1_ASM435869v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004358695.1_ASM435869v1_genomic.fna/checkm_input GCF_004358695.1_ASM435869v1_genomic.fna/checkm_result
[2024-01-24 13:41:44,314] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:44,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:44,333] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:44,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:44,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004358695.1_ASM435869v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:44,334] [INFO] Task started: Blastn
[2024-01-24 13:41:44,334] [INFO] Running command: blastn -query GCF_004358695.1_ASM435869v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb062313-32a4-4e7f-9783-8d275d6748da/dqc_reference/reference_markers_gtdb.fasta -out GCF_004358695.1_ASM435869v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:46,324] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:46,329] [INFO] Selected 23 target genomes.
[2024-01-24 13:41:46,329] [INFO] Target genome list was writen to GCF_004358695.1_ASM435869v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:46,346] [INFO] Task started: fastANI
[2024-01-24 13:41:46,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c0cc86b-a0f6-4ac8-bc3c-0495254b5369/GCF_004358695.1_ASM435869v1_genomic.fna.gz --refList GCF_004358695.1_ASM435869v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004358695.1_ASM435869v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:03,906] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:03,931] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:03,931] [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_004358695.1	s__Palleronia sp004358695	100.0	1102	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900141995.1	s__Palleronia salina	79.7439	560	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_016412875.1	s__Palleronia pontilimi	79.6786	513	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110115.1	s__Palleronia pelagia	79.5872	559	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_900172315.1	s__Palleronia marisminoris	79.4966	505	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000743715.1	s__Palleronia rufa	79.4802	493	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299575.1	s__Palleronia guishaninsula	79.4492	476	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302445.1	s__Palleronia abyssalis	79.0333	483	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111315.1	s__Tranquillimonas rosea	78.8101	495	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	78.7279	434	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142935.1	s__Rhodovulum sp900142935	78.7125	447	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	78.7001	486	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253995.1	s__Palleronia aestuarii	78.6515	422	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	78.6149	436	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004005435.1	s__CCMM004 sp004005435	78.6135	508	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CCMM004	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	78.5997	439	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000153305.1	s__Oceanicola granulosus	78.4266	433	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016446475.1	s__Paracoccus binzhouensis	78.3937	387	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003605175.1	s__IMCC34051 sp003605175	78.2049	423	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	78.1656	419	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCA_001314685.1	s__HLUCCA09 sp001314685	78.137	401	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003564655.1	s__Roseinatronobacter sp003564655	77.6404	303	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseinatronobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000600335.2	s__Rubellimicrobium mesophilum	77.548	319	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:03,933] [INFO] GTDB search result was written to GCF_004358695.1_ASM435869v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:03,934] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:03,938] [INFO] DFAST_QC result json was written to GCF_004358695.1_ASM435869v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:03,939] [INFO] DFAST_QC completed!
[2024-01-24 13:42:03,939] [INFO] Total running time: 0h1m30s