[2024-01-24 12:39:35,328] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:35,330] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:35,330] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5c0af4f-d408-49cb-883e-7ef76026ef21/dqc_reference
[2024-01-24 12:39:36,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:36,562] [INFO] Task started: Prodigal
[2024-01-24 12:39:36,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg01f7ccc4-9e6d-464e-9330-524208187ded/GCF_005222225.1_ASM522222v1_genomic.fna.gz | prodigal -d GCF_005222225.1_ASM522222v1_genomic.fna/cds.fna -a GCF_005222225.1_ASM522222v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:47,279] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:47,279] [INFO] Task started: HMMsearch
[2024-01-24 12:39:47,279] [INFO] Running command: hmmsearch --tblout GCF_005222225.1_ASM522222v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5c0af4f-d408-49cb-883e-7ef76026ef21/dqc_reference/reference_markers.hmm GCF_005222225.1_ASM522222v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:47,580] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:47,582] [INFO] Found 6/6 markers.
[2024-01-24 12:39:47,621] [INFO] Query marker FASTA was written to GCF_005222225.1_ASM522222v1_genomic.fna/markers.fasta
[2024-01-24 12:39:47,621] [INFO] Task started: Blastn
[2024-01-24 12:39:47,621] [INFO] Running command: blastn -query GCF_005222225.1_ASM522222v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5c0af4f-d408-49cb-883e-7ef76026ef21/dqc_reference/reference_markers.fasta -out GCF_005222225.1_ASM522222v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:48,390] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:48,395] [INFO] Selected 22 target genomes.
[2024-01-24 12:39:48,396] [INFO] Target genome list was writen to GCF_005222225.1_ASM522222v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:48,406] [INFO] Task started: fastANI
[2024-01-24 12:39:48,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg01f7ccc4-9e6d-464e-9330-524208187ded/GCF_005222225.1_ASM522222v1_genomic.fna.gz --refList GCF_005222225.1_ASM522222v1_genomic.fna/target_genomes.txt --output GCF_005222225.1_ASM522222v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:03,552] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:03,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5c0af4f-d408-49cb-883e-7ef76026ef21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:03,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5c0af4f-d408-49cb-883e-7ef76026ef21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:03,568] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:03,569] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:03,569] [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
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	100.0	1374	1374	95	conclusive
Salinimonas iocasae	strain=KX18D6	GCA_006228385.1	2572577	2572577	type	True	79.9197	320	1374	95	below_threshold
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	79.1938	343	1374	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	78.9034	151	1374	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	78.8459	163	1374	95	below_threshold
Alteromonas antoniana	strain=MD_567	GCA_019249295.1	2803813	2803813	type	True	78.6403	237	1374	95	below_threshold
Salinimonas chungwhensis	strain=DSM 16280	GCA_000378185.1	265425	265425	type	True	78.6253	289	1374	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	78.532	160	1374	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	78.4522	225	1374	95	below_threshold
Alteromonas pelagimontana	strain=5.12	GCA_002499975.2	1858656	1858656	type	True	78.4325	172	1374	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	78.3072	234	1374	95	below_threshold
Alteromonas aestuariivivens	strain=KCTC 52655	GCA_003367475.1	1938339	1938339	type	True	78.2482	201	1374	95	below_threshold
Shigella sonnei	strain=ATCC 29930	GCA_002950395.1	624	624	type	True	78.246	56	1374	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	78.2442	212	1374	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	78.1925	215	1374	95	below_threshold
Alteromonas lipolytica	strain=CGMCC 1.15735	GCA_014643555.1	1856405	1856405	type	True	77.8245	209	1374	95	below_threshold
Vibrio albus	strain=E4404	GCA_003144035.1	2200953	2200953	type	True	76.3033	52	1374	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_016918075.2	2793282	2793282	type	True	76.1484	61	1374	95	below_threshold
Rheinheimera maricola	strain=MA-13	GCA_017824735.1	2793282	2793282	type	True	76.0506	60	1374	95	below_threshold
Oceanimonas baumannii	strain=DSM 15594	GCA_004365405.1	129578	129578	type	True	75.8121	55	1374	95	below_threshold
Oceanimonas baumannii	strain=ATCC 700832	GCA_002245495.1	129578	129578	type	True	75.8113	55	1374	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:03,571] [INFO] DFAST Taxonomy check result was written to GCF_005222225.1_ASM522222v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:03,571] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:03,571] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:03,572] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5c0af4f-d408-49cb-883e-7ef76026ef21/dqc_reference/checkm_data
[2024-01-24 12:40:03,573] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:03,618] [INFO] Task started: CheckM
[2024-01-24 12:40:03,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005222225.1_ASM522222v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005222225.1_ASM522222v1_genomic.fna/checkm_input GCF_005222225.1_ASM522222v1_genomic.fna/checkm_result
[2024-01-24 12:40:41,142] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:41,143] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:41,168] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:41,169] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:41,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005222225.1_ASM522222v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:41,169] [INFO] Task started: Blastn
[2024-01-24 12:40:41,170] [INFO] Running command: blastn -query GCF_005222225.1_ASM522222v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5c0af4f-d408-49cb-883e-7ef76026ef21/dqc_reference/reference_markers_gtdb.fasta -out GCF_005222225.1_ASM522222v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:42,353] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:42,356] [INFO] Selected 18 target genomes.
[2024-01-24 12:40:42,357] [INFO] Target genome list was writen to GCF_005222225.1_ASM522222v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:42,369] [INFO] Task started: fastANI
[2024-01-24 12:40:42,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg01f7ccc4-9e6d-464e-9330-524208187ded/GCF_005222225.1_ASM522222v1_genomic.fna.gz --refList GCF_005222225.1_ASM522222v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005222225.1_ASM522222v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:55,885] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:55,905] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:55,906] [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_005222225.1	s__Alteromonas lutimaris	100.0	1374	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006228385.1	s__Alteromonas iocasae	80.0131	321	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003429285.1	s__Alteromonas sediminis	79.25	353	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.07	99.07	0.95	0.95	2	-
GCF_014750655.1	s__Alteromonas profundi_A	79.2074	342	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443615.1	s__Alteromonas sp003443615	79.1528	156	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003584565.2	s__Alteromonas sp002729795	79.0719	265	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.21	97.21	0.92	0.92	2	-
GCA_019249245.1	s__Alteromonas lipotrueiana	78.9003	281	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020585.3	s__Alteromonas mediterranea	78.8576	162	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	-
GCF_015644725.1	s__Alteromonas sp015644725	78.7803	406	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378185.1	s__Alteromonas chungwhensis	78.6493	288	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019249295.1	s__Alteromonas antoniana	78.6238	237	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002499975.2	s__Alteromonas pelagimontana	78.53	172	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	0.99	0.99	2	-
GCA_018222405.1	s__Alteromonas sp018222405	78.4808	196	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538325.1	s__Alteromonas sp006538325	78.3291	132	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014651815.1	s__Alteromonas halophila	78.3009	235	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367475.1	s__Alteromonas aestuariivivens	78.2482	201	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794925.1	s__Alteromonas sp017794925	78.0638	169	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339125.1	s__Alteromonas sp002335925	77.5395	205	1374	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:55,908] [INFO] GTDB search result was written to GCF_005222225.1_ASM522222v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:55,908] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:55,914] [INFO] DFAST_QC result json was written to GCF_005222225.1_ASM522222v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:55,914] [INFO] DFAST_QC completed!
[2024-01-24 12:40:55,914] [INFO] Total running time: 0h1m21s