[2024-01-24 14:05:47,803] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:47,806] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:47,806] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a9d1fe0-001e-447c-b37c-b538a1561f42/dqc_reference
[2024-01-24 14:05:49,194] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:49,195] [INFO] Task started: Prodigal
[2024-01-24 14:05:49,196] [INFO] Running command: gunzip -c /var/lib/cwl/stgb557d1d8-24b8-43ae-8727-d35d8b8af7ec/GCF_003253995.1_ASM325399v1_genomic.fna.gz | prodigal -d GCF_003253995.1_ASM325399v1_genomic.fna/cds.fna -a GCF_003253995.1_ASM325399v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:02,439] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:02,440] [INFO] Task started: HMMsearch
[2024-01-24 14:06:02,440] [INFO] Running command: hmmsearch --tblout GCF_003253995.1_ASM325399v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a9d1fe0-001e-447c-b37c-b538a1561f42/dqc_reference/reference_markers.hmm GCF_003253995.1_ASM325399v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:02,736] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:02,738] [INFO] Found 6/6 markers.
[2024-01-24 14:06:02,780] [INFO] Query marker FASTA was written to GCF_003253995.1_ASM325399v1_genomic.fna/markers.fasta
[2024-01-24 14:06:02,780] [INFO] Task started: Blastn
[2024-01-24 14:06:02,780] [INFO] Running command: blastn -query GCF_003253995.1_ASM325399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a9d1fe0-001e-447c-b37c-b538a1561f42/dqc_reference/reference_markers.fasta -out GCF_003253995.1_ASM325399v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:03,786] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:03,789] [INFO] Selected 24 target genomes.
[2024-01-24 14:06:03,790] [INFO] Target genome list was writen to GCF_003253995.1_ASM325399v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:03,794] [INFO] Task started: fastANI
[2024-01-24 14:06:03,794] [INFO] Running command: fastANI --query /var/lib/cwl/stgb557d1d8-24b8-43ae-8727-d35d8b8af7ec/GCF_003253995.1_ASM325399v1_genomic.fna.gz --refList GCF_003253995.1_ASM325399v1_genomic.fna/target_genomes.txt --output GCF_003253995.1_ASM325399v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:21,788] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:21,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a9d1fe0-001e-447c-b37c-b538a1561f42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:21,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a9d1fe0-001e-447c-b37c-b538a1561f42/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:21,809] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:21,810] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:21,810] [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
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	100.0	1469	1477	95	conclusive
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	78.9359	414	1477	95	below_threshold
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	78.895	473	1477	95	below_threshold
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	78.6314	479	1477	95	below_threshold
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	78.5655	443	1477	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.5026	441	1477	95	below_threshold
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	78.4925	432	1477	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.4808	433	1477	95	below_threshold
Limimaricola hongkongensis	strain=DSM 17492	GCA_000600975.2	278132	278132	type	True	78.2145	390	1477	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.1703	457	1477	95	below_threshold
Roseitranquillus sediminis	strain=MCCB 386	GCA_016918935.1	2809051	2809051	type	True	78.1605	353	1477	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.1404	393	1477	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	78.1251	415	1477	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	77.9642	403	1477	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	77.9457	404	1477	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	77.7745	357	1477	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	77.6839	384	1477	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.5683	346	1477	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.557	325	1477	95	below_threshold
Paenimaribius caenipelagi	strain=JBTF-M29	GCA_007004065.1	2489174	2489174	type	True	77.4043	215	1477	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.255	256	1477	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.1113	264	1477	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	77.0442	225	1477	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	76.8896	183	1477	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:21,812] [INFO] DFAST Taxonomy check result was written to GCF_003253995.1_ASM325399v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:21,813] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:21,813] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:21,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a9d1fe0-001e-447c-b37c-b538a1561f42/dqc_reference/checkm_data
[2024-01-24 14:06:21,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:21,859] [INFO] Task started: CheckM
[2024-01-24 14:06:21,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003253995.1_ASM325399v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003253995.1_ASM325399v1_genomic.fna/checkm_input GCF_003253995.1_ASM325399v1_genomic.fna/checkm_result
[2024-01-24 14:07:03,253] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:03,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:03,277] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:03,277] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:03,278] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003253995.1_ASM325399v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:03,278] [INFO] Task started: Blastn
[2024-01-24 14:07:03,278] [INFO] Running command: blastn -query GCF_003253995.1_ASM325399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a9d1fe0-001e-447c-b37c-b538a1561f42/dqc_reference/reference_markers_gtdb.fasta -out GCF_003253995.1_ASM325399v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:04,944] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:04,950] [INFO] Selected 21 target genomes.
[2024-01-24 14:07:04,950] [INFO] Target genome list was writen to GCF_003253995.1_ASM325399v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:04,963] [INFO] Task started: fastANI
[2024-01-24 14:07:04,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgb557d1d8-24b8-43ae-8727-d35d8b8af7ec/GCF_003253995.1_ASM325399v1_genomic.fna.gz --refList GCF_003253995.1_ASM325399v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003253995.1_ASM325399v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:20,507] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:20,535] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:20,535] [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_003253995.1	s__Palleronia aestuarii	100.0	1469	1477	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_000743715.1	s__Palleronia rufa	78.9288	414	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141995.1	s__Palleronia salina	78.9231	472	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_900110115.1	s__Palleronia pelagia	78.6399	478	1477	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	78.5198	429	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004358695.1	s__Palleronia sp004358695	78.504	441	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016412875.1	s__Palleronia pontilimi	78.4746	464	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	78.4635	505	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009835145.1	s__Profundibacterium mesophilum	78.4344	405	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	78.3805	416	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	78.1782	456	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004005435.1	s__CCMM004 sp004005435	78.1194	399	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CCMM004	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299575.1	s__Palleronia guishaninsula	78.0906	379	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	77.9482	403	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003605175.1	s__IMCC34051 sp003605175	77.8713	394	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	77.8487	318	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034985.1	s__Cereibacter changlensis	77.775	356	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
GCA_008933605.1	s__Albidovulum sp008933605	77.7026	307	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	77.2918	352	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018279165.1	s__Falsirhodobacter sp018279165	77.192	236	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176485.1	s__Primorskyibacter flagellatus_A	76.5598	172	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:20,537] [INFO] GTDB search result was written to GCF_003253995.1_ASM325399v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:20,538] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:20,543] [INFO] DFAST_QC result json was written to GCF_003253995.1_ASM325399v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:20,543] [INFO] DFAST_QC completed!
[2024-01-24 14:07:20,543] [INFO] Total running time: 0h1m33s