[2024-01-24 14:21:50,839] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,840] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,841] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3423410-8e5a-4f5c-92eb-c6b2c53491b5/dqc_reference
[2024-01-24 14:21:52,276] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:52,277] [INFO] Task started: Prodigal
[2024-01-24 14:21:52,277] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e247be8-7395-49d9-b6f2-c3a29cd27b4a/GCF_009835145.1_ASM983514v1_genomic.fna.gz | prodigal -d GCF_009835145.1_ASM983514v1_genomic.fna/cds.fna -a GCF_009835145.1_ASM983514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:02,335] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:02,335] [INFO] Task started: HMMsearch
[2024-01-24 14:22:02,336] [INFO] Running command: hmmsearch --tblout GCF_009835145.1_ASM983514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3423410-8e5a-4f5c-92eb-c6b2c53491b5/dqc_reference/reference_markers.hmm GCF_009835145.1_ASM983514v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:02,634] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:02,635] [INFO] Found 6/6 markers.
[2024-01-24 14:22:02,667] [INFO] Query marker FASTA was written to GCF_009835145.1_ASM983514v1_genomic.fna/markers.fasta
[2024-01-24 14:22:02,667] [INFO] Task started: Blastn
[2024-01-24 14:22:02,667] [INFO] Running command: blastn -query GCF_009835145.1_ASM983514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3423410-8e5a-4f5c-92eb-c6b2c53491b5/dqc_reference/reference_markers.fasta -out GCF_009835145.1_ASM983514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:03,719] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:03,722] [INFO] Selected 29 target genomes.
[2024-01-24 14:22:03,723] [INFO] Target genome list was writen to GCF_009835145.1_ASM983514v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:03,737] [INFO] Task started: fastANI
[2024-01-24 14:22:03,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e247be8-7395-49d9-b6f2-c3a29cd27b4a/GCF_009835145.1_ASM983514v1_genomic.fna.gz --refList GCF_009835145.1_ASM983514v1_genomic.fna/target_genomes.txt --output GCF_009835145.1_ASM983514v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:25,205] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:25,206] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3423410-8e5a-4f5c-92eb-c6b2c53491b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:25,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3423410-8e5a-4f5c-92eb-c6b2c53491b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:25,229] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:22:25,229] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:22:25,230] [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
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.1417	484	1085	95	below_threshold
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	79.072	472	1085	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.9497	422	1085	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	78.9167	454	1085	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.8932	401	1085	95	below_threshold
Limimaricola soesokkakensis	strain=DSM 29956	GCA_003014435.1	1343159	1343159	type	True	78.8244	466	1085	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.7487	432	1085	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.7478	434	1085	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.7037	444	1085	95	below_threshold
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	78.6459	389	1085	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.6397	337	1085	95	below_threshold
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	78.6222	383	1085	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	78.5358	397	1085	95	below_threshold
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	78.4275	393	1085	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	78.3729	404	1085	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.3526	401	1085	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	78.3029	400	1085	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.264	352	1085	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2553	363	1085	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	78.2462	376	1085	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.027	401	1085	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	78.0017	394	1085	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	77.9703	407	1085	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.9546	373	1085	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	77.926	299	1085	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	77.8664	304	1085	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.8479	379	1085	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	77.6393	328	1085	95	below_threshold
Paenimaribius caenipelagi	strain=JBTF-M29	GCA_007004065.1	2489174	2489174	type	True	77.5546	230	1085	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:25,231] [INFO] DFAST Taxonomy check result was written to GCF_009835145.1_ASM983514v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:25,232] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:25,232] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:25,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3423410-8e5a-4f5c-92eb-c6b2c53491b5/dqc_reference/checkm_data
[2024-01-24 14:22:25,234] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:25,272] [INFO] Task started: CheckM
[2024-01-24 14:22:25,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009835145.1_ASM983514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009835145.1_ASM983514v1_genomic.fna/checkm_input GCF_009835145.1_ASM983514v1_genomic.fna/checkm_result
[2024-01-24 14:22:59,146] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:59,147] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:59,166] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:59,167] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:59,167] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009835145.1_ASM983514v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:59,168] [INFO] Task started: Blastn
[2024-01-24 14:22:59,168] [INFO] Running command: blastn -query GCF_009835145.1_ASM983514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3423410-8e5a-4f5c-92eb-c6b2c53491b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_009835145.1_ASM983514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:00,964] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:00,969] [INFO] Selected 22 target genomes.
[2024-01-24 14:23:00,970] [INFO] Target genome list was writen to GCF_009835145.1_ASM983514v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:00,995] [INFO] Task started: fastANI
[2024-01-24 14:23:00,995] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e247be8-7395-49d9-b6f2-c3a29cd27b4a/GCF_009835145.1_ASM983514v1_genomic.fna.gz --refList GCF_009835145.1_ASM983514v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009835145.1_ASM983514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:16,866] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:16,883] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:16,884] [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_009835145.1	s__Profundibacterium mesophilum	100.0	1083	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002723615.1	s__Limimaricola cinnabarinus_B	79.3612	480	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	79.1283	486	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016412875.1	s__Palleronia pontilimi	78.8954	448	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195545.1	s__Limimaricola variabilis	78.8845	458	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072125.1	s__Roseovarius sediminicola	78.8782	331	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	78.8018	486	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	78.6731	382	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111315.1	s__Tranquillimonas rosea	78.6648	460	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172315.1	s__Palleronia marisminoris	78.6328	382	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	0.99	0.99	2	-
GCA_004005435.1	s__CCMM004 sp004005435	78.5663	467	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CCMM004	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011175.1	s__Tranquillimonas littorinae	78.5352	426	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253995.1	s__Palleronia aestuarii	78.4275	393	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842985.1	s__Roseovarius sp002842985	78.3496	324	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122205.1	s__QEYE01 sp003122205	78.3291	358	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QEYE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003605175.1	s__IMCC34051 sp003605175	78.3232	393	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	78.2994	332	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299575.1	s__Palleronia guishaninsula	78.2936	399	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002720475.1	s__Roseovarius sp002720475	78.2411	299	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.80	99.74	0.82	0.71	3	-
GCA_001314655.1	s__Salibaculum sp001314655	78.1968	361	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	78.0111	393	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_007004065.1	s__Palleronia caenipelagi	77.5812	228	1085	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:16,886] [INFO] GTDB search result was written to GCF_009835145.1_ASM983514v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:16,887] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:16,894] [INFO] DFAST_QC result json was written to GCF_009835145.1_ASM983514v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:16,894] [INFO] DFAST_QC completed!
[2024-01-24 14:23:16,894] [INFO] Total running time: 0h1m26s