[2024-01-25 19:36:35,591] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:36:35,594] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:36:35,594] [INFO] DQC Reference Directory: /var/lib/cwl/stgfed3eeb6-0c41-4d20-a9d3-cdea0bf8f995/dqc_reference
[2024-01-25 19:36:36,755] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:36:36,755] [INFO] Task started: Prodigal
[2024-01-25 19:36:36,755] [INFO] Running command: gunzip -c /var/lib/cwl/stg062a8d1a-9412-4c4c-9ec6-500c5720caf0/GCF_026719705.1_ASM2671970v1_genomic.fna.gz | prodigal -d GCF_026719705.1_ASM2671970v1_genomic.fna/cds.fna -a GCF_026719705.1_ASM2671970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:36:46,590] [INFO] Task succeeded: Prodigal
[2024-01-25 19:36:46,591] [INFO] Task started: HMMsearch
[2024-01-25 19:36:46,591] [INFO] Running command: hmmsearch --tblout GCF_026719705.1_ASM2671970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfed3eeb6-0c41-4d20-a9d3-cdea0bf8f995/dqc_reference/reference_markers.hmm GCF_026719705.1_ASM2671970v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:36:46,794] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:36:46,795] [INFO] Found 6/6 markers.
[2024-01-25 19:36:46,823] [INFO] Query marker FASTA was written to GCF_026719705.1_ASM2671970v1_genomic.fna/markers.fasta
[2024-01-25 19:36:46,823] [INFO] Task started: Blastn
[2024-01-25 19:36:46,824] [INFO] Running command: blastn -query GCF_026719705.1_ASM2671970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfed3eeb6-0c41-4d20-a9d3-cdea0bf8f995/dqc_reference/reference_markers.fasta -out GCF_026719705.1_ASM2671970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:47,627] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:47,630] [INFO] Selected 23 target genomes.
[2024-01-25 19:36:47,630] [INFO] Target genome list was writen to GCF_026719705.1_ASM2671970v1_genomic.fna/target_genomes.txt
[2024-01-25 19:36:47,642] [INFO] Task started: fastANI
[2024-01-25 19:36:47,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg062a8d1a-9412-4c4c-9ec6-500c5720caf0/GCF_026719705.1_ASM2671970v1_genomic.fna.gz --refList GCF_026719705.1_ASM2671970v1_genomic.fna/target_genomes.txt --output GCF_026719705.1_ASM2671970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:02,103] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:02,103] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfed3eeb6-0c41-4d20-a9d3-cdea0bf8f995/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:02,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfed3eeb6-0c41-4d20-a9d3-cdea0bf8f995/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:02,116] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:37:02,116] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:37:02,116] [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
Kordiimonas marina	strain=A6E486	GCA_023006325.1	2872312	2872312	type	True	78.1622	329	1178	95	below_threshold
Kordiimonas gwangyangensis	strain=DSM 19435	GCA_000375545.1	288022	288022	type	True	77.8037	246	1178	95	below_threshold
Kordiimonas lacus	strain=CGMCC 1.9109	GCA_900101935.1	637679	637679	type	True	77.4019	231	1178	95	below_threshold
Kordiimonas lacus	strain=S3-22	GCA_001550055.1	637679	637679	type	True	77.3468	237	1178	95	below_threshold
Kordiimonas lipolytica	strain=M41	GCA_001550065.1	1662421	1662421	type	True	77.2585	227	1178	95	below_threshold
Eilatimonas milleporae	strain=DSM 25217	GCA_003688555.1	911205	911205	type	True	76.7911	155	1178	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.6607	102	1178	95	below_threshold
Hankyongella ginsenosidimutans	strain=W1-2-3	GCA_005144965.1	1763828	1763828	type	True	76.442	96	1178	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.4172	117	1178	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	76.3742	88	1178	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.2766	91	1178	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	76.0893	74	1178	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.0758	80	1178	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	76.0103	82	1178	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.0011	78	1178	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	75.9782	96	1178	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	75.9667	83	1178	95	below_threshold
Sphingobium xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	75.9465	78	1178	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	75.8752	79	1178	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	75.8559	81	1178	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	75.8433	78	1178	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	75.6074	68	1178	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:02,117] [INFO] DFAST Taxonomy check result was written to GCF_026719705.1_ASM2671970v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:02,118] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:02,118] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:02,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfed3eeb6-0c41-4d20-a9d3-cdea0bf8f995/dqc_reference/checkm_data
[2024-01-25 19:37:02,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:02,153] [INFO] Task started: CheckM
[2024-01-25 19:37:02,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026719705.1_ASM2671970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026719705.1_ASM2671970v1_genomic.fna/checkm_input GCF_026719705.1_ASM2671970v1_genomic.fna/checkm_result
[2024-01-25 19:37:34,044] [INFO] Task succeeded: CheckM
[2024-01-25 19:37:34,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:37:34,058] [INFO] ===== Completeness check finished =====
[2024-01-25 19:37:34,058] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:37:34,058] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026719705.1_ASM2671970v1_genomic.fna/markers.fasta)
[2024-01-25 19:37:34,059] [INFO] Task started: Blastn
[2024-01-25 19:37:34,059] [INFO] Running command: blastn -query GCF_026719705.1_ASM2671970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfed3eeb6-0c41-4d20-a9d3-cdea0bf8f995/dqc_reference/reference_markers_gtdb.fasta -out GCF_026719705.1_ASM2671970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:35,629] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:35,631] [INFO] Selected 19 target genomes.
[2024-01-25 19:37:35,632] [INFO] Target genome list was writen to GCF_026719705.1_ASM2671970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:37:35,683] [INFO] Task started: fastANI
[2024-01-25 19:37:35,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg062a8d1a-9412-4c4c-9ec6-500c5720caf0/GCF_026719705.1_ASM2671970v1_genomic.fna.gz --refList GCF_026719705.1_ASM2671970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026719705.1_ASM2671970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:37:48,654] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:48,664] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:37:48,665] [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
GCA_006226495.1	s__Kordiimonas sp006226495	78.2003	390	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000375545.1	s__Kordiimonas gwangyangensis	77.8175	245	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	99.96	99.96	1.00	1.00	2	-
GCF_001550055.1	s__Kordiimonas lacus	77.3468	237	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	98.68	97.35	0.95	0.90	3	-
GCF_001550065.1	s__Kordiimonas lipolytica	77.2585	227	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688555.1	s__Eilatimonas milleporae	76.7911	155	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Eilatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013372925.1	s__Kordiimonas sp013372925	76.6086	94	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961745.1	s__BRH-c57 sp000961745	76.4468	74	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__BRH-c57	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013372975.1	s__Kordiimonas sp013372975	76.421	125	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762095.1	s__Parvibaculum indicum	76.395	90	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	76.3771	89	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	76.3026	79	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787695.1	s__Paracoccus sp000787695	76.0526	69	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642695.1	s__Parvibaculum sp017642695	75.9989	71	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCF_900106695.1	s__Albimonas donghaensis	75.9667	83	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	97.11	97.08	0.90	0.88	3	-
GCF_012395815.1	s__Roseicyclus sp012395815	75.8504	79	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601025.1	s__Rhodospira navarrensis	75.8343	71	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128995.1	s__Loktanella atrilutea	75.6074	68	1178	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:37:48,666] [INFO] GTDB search result was written to GCF_026719705.1_ASM2671970v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:37:48,666] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:37:48,670] [INFO] DFAST_QC result json was written to GCF_026719705.1_ASM2671970v1_genomic.fna/dqc_result.json
[2024-01-25 19:37:48,670] [INFO] DFAST_QC completed!
[2024-01-25 19:37:48,670] [INFO] Total running time: 0h1m13s