[2024-01-25 17:34:07,124] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,128] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,129] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7566c89-0ad5-49c4-9411-5dda660cd264/dqc_reference
[2024-01-25 17:34:08,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:08,951] [INFO] Task started: Prodigal
[2024-01-25 17:34:08,951] [INFO] Running command: gunzip -c /var/lib/cwl/stgee3149a2-b739-46a8-bdff-6b2ffe177c55/GCF_009830125.1_ASM983012v1_genomic.fna.gz | prodigal -d GCF_009830125.1_ASM983012v1_genomic.fna/cds.fna -a GCF_009830125.1_ASM983012v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:18,512] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:18,513] [INFO] Task started: HMMsearch
[2024-01-25 17:34:18,513] [INFO] Running command: hmmsearch --tblout GCF_009830125.1_ASM983012v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7566c89-0ad5-49c4-9411-5dda660cd264/dqc_reference/reference_markers.hmm GCF_009830125.1_ASM983012v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:18,766] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:18,767] [INFO] Found 6/6 markers.
[2024-01-25 17:34:18,797] [INFO] Query marker FASTA was written to GCF_009830125.1_ASM983012v1_genomic.fna/markers.fasta
[2024-01-25 17:34:18,798] [INFO] Task started: Blastn
[2024-01-25 17:34:18,798] [INFO] Running command: blastn -query GCF_009830125.1_ASM983012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7566c89-0ad5-49c4-9411-5dda660cd264/dqc_reference/reference_markers.fasta -out GCF_009830125.1_ASM983012v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:19,788] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:19,791] [INFO] Selected 27 target genomes.
[2024-01-25 17:34:19,791] [INFO] Target genome list was writen to GCF_009830125.1_ASM983012v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:19,816] [INFO] Task started: fastANI
[2024-01-25 17:34:19,816] [INFO] Running command: fastANI --query /var/lib/cwl/stgee3149a2-b739-46a8-bdff-6b2ffe177c55/GCF_009830125.1_ASM983012v1_genomic.fna.gz --refList GCF_009830125.1_ASM983012v1_genomic.fna/target_genomes.txt --output GCF_009830125.1_ASM983012v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:40,034] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:40,034] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7566c89-0ad5-49c4-9411-5dda660cd264/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:40,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7566c89-0ad5-49c4-9411-5dda660cd264/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:40,050] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:34:40,051] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:40,051] [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
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	100.0	1222	1223	95	conclusive
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	78.6844	460	1223	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	78.6135	468	1223	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.3496	408	1223	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	78.3009	314	1223	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.2738	403	1223	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.2462	424	1223	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	78.241	354	1223	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.2391	353	1223	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.2213	371	1223	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	78.2206	395	1223	95	below_threshold
Pseudooceanicola nanhaiensis	strain=CGMCC 1.6293	GCA_014645095.1	375761	375761	type	True	78.1088	391	1223	95	below_threshold
Limimaricola variabilis	strain=CECT 8572	GCA_014195545.1	1492771	1492771	type	True	78.1078	346	1223	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.0933	393	1223	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_000152805.1	404236	404236	type	True	78.0788	360	1223	95	below_threshold
Pseudooceanicola nanhaiensis	strain=DSM 18065	GCA_000688295.1	375761	375761	type	True	78.0767	391	1223	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	78.0708	371	1223	95	below_threshold
Maritimibacter alkaliphilus	strain=HTCC2654	GCA_008124775.1	404236	404236	type	True	78.0263	354	1223	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.0239	401	1223	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	77.9898	344	1223	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.9794	345	1223	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.5646	305	1223	95	below_threshold
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	77.547	267	1223	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	77.5047	288	1223	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.3596	270	1223	95	below_threshold
Qingshengfaniella alkalisoli	strain=LN3S51	GCA_007855645.1	2599296	2599296	type	True	77.3035	187	1223	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.3026	272	1223	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:40,053] [INFO] DFAST Taxonomy check result was written to GCF_009830125.1_ASM983012v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:40,054] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:40,055] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:40,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7566c89-0ad5-49c4-9411-5dda660cd264/dqc_reference/checkm_data
[2024-01-25 17:34:40,058] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:40,097] [INFO] Task started: CheckM
[2024-01-25 17:34:40,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009830125.1_ASM983012v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009830125.1_ASM983012v1_genomic.fna/checkm_input GCF_009830125.1_ASM983012v1_genomic.fna/checkm_result
[2024-01-25 17:35:12,646] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:12,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:12,678] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:12,678] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:12,679] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009830125.1_ASM983012v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:12,679] [INFO] Task started: Blastn
[2024-01-25 17:35:12,679] [INFO] Running command: blastn -query GCF_009830125.1_ASM983012v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7566c89-0ad5-49c4-9411-5dda660cd264/dqc_reference/reference_markers_gtdb.fasta -out GCF_009830125.1_ASM983012v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:14,605] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:14,609] [INFO] Selected 24 target genomes.
[2024-01-25 17:35:14,609] [INFO] Target genome list was writen to GCF_009830125.1_ASM983012v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:14,622] [INFO] Task started: fastANI
[2024-01-25 17:35:14,622] [INFO] Running command: fastANI --query /var/lib/cwl/stgee3149a2-b739-46a8-bdff-6b2ffe177c55/GCF_009830125.1_ASM983012v1_genomic.fna.gz --refList GCF_009830125.1_ASM983012v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009830125.1_ASM983012v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:34,966] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:34,980] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:34,980] [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_009830125.1	s__GH1-50 sp009830125	100.0	1222	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018139985.1	s__JAGSOU01 sp018139985	78.6922	420	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148765.1	s__Silicimonas algicola	78.6135	468	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Silicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	78.4142	421	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	78.4029	413	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	78.3431	466	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	78.3267	385	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	78.2694	422	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014195545.1	s__Limimaricola variabilis	78.1291	344	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	78.1274	354	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018145.1	s__Dinoroseobacter shibae	78.0937	368	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Dinoroseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000688295.1	s__Pseudooceanicola nanhaiensis	78.0728	392	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900142295.1	s__Vannielia litorea	78.0637	347	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Vannielia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	78.0101	419	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000768315.1	s__Pseudooceanicola atlanticus	78.0036	358	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.92	0.92	2	-
GCF_001975705.1	s__Salipiger abyssi	77.9778	398	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	77.9759	254	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013184805.1	s__Rhodobacter_B sp013184805	77.9213	362	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122205.1	s__QEYE01 sp003122205	77.8532	352	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QEYE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002465.1	s__JABDJO01 sp013002465	77.645	277	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABDJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253995.1	s__Palleronia aestuarii	77.5472	267	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.4497	279	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014075275.1	s__Boseongicola sp014075275	77.4134	208	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Boseongicola	95.0	99.87	99.87	0.99	0.99	2	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	77.3234	270	1223	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:34,981] [INFO] GTDB search result was written to GCF_009830125.1_ASM983012v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:34,982] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:34,990] [INFO] DFAST_QC result json was written to GCF_009830125.1_ASM983012v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:34,990] [INFO] DFAST_QC completed!
[2024-01-25 17:35:34,990] [INFO] Total running time: 0h1m28s