[2024-01-25 18:12:35,333] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:35,334] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:35,334] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6049d58-0170-4536-ba29-c36f2dc546c7/dqc_reference
[2024-01-25 18:12:36,484] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:36,484] [INFO] Task started: Prodigal
[2024-01-25 18:12:36,485] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a9f7c6a-8c6c-4e35-8dee-8b73f395fbda/GCF_018224955.1_ASM1822495v1_genomic.fna.gz | prodigal -d GCF_018224955.1_ASM1822495v1_genomic.fna/cds.fna -a GCF_018224955.1_ASM1822495v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:52,043] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:52,044] [INFO] Task started: HMMsearch
[2024-01-25 18:12:52,044] [INFO] Running command: hmmsearch --tblout GCF_018224955.1_ASM1822495v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6049d58-0170-4536-ba29-c36f2dc546c7/dqc_reference/reference_markers.hmm GCF_018224955.1_ASM1822495v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:52,270] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:52,271] [INFO] Found 6/6 markers.
[2024-01-25 18:12:52,313] [INFO] Query marker FASTA was written to GCF_018224955.1_ASM1822495v1_genomic.fna/markers.fasta
[2024-01-25 18:12:52,314] [INFO] Task started: Blastn
[2024-01-25 18:12:52,314] [INFO] Running command: blastn -query GCF_018224955.1_ASM1822495v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6049d58-0170-4536-ba29-c36f2dc546c7/dqc_reference/reference_markers.fasta -out GCF_018224955.1_ASM1822495v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:53,124] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:53,127] [INFO] Selected 24 target genomes.
[2024-01-25 18:12:53,128] [INFO] Target genome list was writen to GCF_018224955.1_ASM1822495v1_genomic.fna/target_genomes.txt
[2024-01-25 18:12:53,147] [INFO] Task started: fastANI
[2024-01-25 18:12:53,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a9f7c6a-8c6c-4e35-8dee-8b73f395fbda/GCF_018224955.1_ASM1822495v1_genomic.fna.gz --refList GCF_018224955.1_ASM1822495v1_genomic.fna/target_genomes.txt --output GCF_018224955.1_ASM1822495v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:14,756] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:14,757] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6049d58-0170-4536-ba29-c36f2dc546c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:14,757] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6049d58-0170-4536-ba29-c36f2dc546c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:14,771] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:13:14,771] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:13:14,771] [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
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	80.3963	818	1604	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	80.2658	835	1604	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	79.7008	709	1604	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	79.6462	722	1604	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	79.5427	670	1604	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	79.5353	687	1604	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	79.4804	670	1604	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	79.3559	613	1604	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	79.2665	615	1604	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	79.2414	663	1604	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	79.2245	697	1604	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	79.2097	702	1604	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	79.1087	680	1604	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.1018	550	1604	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	79.0825	581	1604	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	79.0771	549	1604	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	79.0231	517	1604	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.9788	582	1604	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	78.8355	529	1604	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	78.7691	546	1604	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.7096	545	1604	95	below_threshold
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	78.6243	558	1604	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	78.4674	560	1604	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	78.1671	428	1604	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:14,772] [INFO] DFAST Taxonomy check result was written to GCF_018224955.1_ASM1822495v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:14,773] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:14,773] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:14,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6049d58-0170-4536-ba29-c36f2dc546c7/dqc_reference/checkm_data
[2024-01-25 18:13:14,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:14,819] [INFO] Task started: CheckM
[2024-01-25 18:13:14,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018224955.1_ASM1822495v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018224955.1_ASM1822495v1_genomic.fna/checkm_input GCF_018224955.1_ASM1822495v1_genomic.fna/checkm_result
[2024-01-25 18:14:08,414] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:08,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:08,436] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:08,437] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:08,439] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018224955.1_ASM1822495v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:08,439] [INFO] Task started: Blastn
[2024-01-25 18:14:08,439] [INFO] Running command: blastn -query GCF_018224955.1_ASM1822495v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6049d58-0170-4536-ba29-c36f2dc546c7/dqc_reference/reference_markers_gtdb.fasta -out GCF_018224955.1_ASM1822495v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:09,855] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:09,858] [INFO] Selected 22 target genomes.
[2024-01-25 18:14:09,858] [INFO] Target genome list was writen to GCF_018224955.1_ASM1822495v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:09,876] [INFO] Task started: fastANI
[2024-01-25 18:14:09,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a9f7c6a-8c6c-4e35-8dee-8b73f395fbda/GCF_018224955.1_ASM1822495v1_genomic.fna.gz --refList GCF_018224955.1_ASM1822495v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018224955.1_ASM1822495v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:32,680] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:32,693] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:14:32,693] [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_018224955.1	s__Aestuariicoccus sp018224955	100.0	1602	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900184945.1	s__Maliponia aquimaris	81.6703	947	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	81.3637	863	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	80.7048	766	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255395.1	s__AWRV01 sp017255395	80.4411	743	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101505.1	s__Mameliella alba	80.2727	834	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCA_016806125.1	s__AWRV01 sp000504185	80.1925	757	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000442255.1	s__Salipiger mucosus	80.1283	695	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	80.0051	817	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	79.897	704	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	79.8648	674	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	79.7791	758	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002300555.1	s__Salipiger sp002300555	79.6778	497	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	79.5407	689	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_900100085.1	s__Salipiger marinus	79.5164	673	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.13	98.13	0.95	0.95	2	-
GCF_015223355.1	s__Salipiger pacificus_B	79.5098	686	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169415.1	s__Sagittula stellata	79.4232	699	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003111685.1	s__Salipiger pacificus_A	79.3892	643	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_900116195.1	s__Salipiger pacificus	79.2063	703	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004339675.1	s__Rhodovulum steppense	79.1024	546	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	79.0248	589	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111315.1	s__Tranquillimonas rosea	78.4135	512	1604	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:32,694] [INFO] GTDB search result was written to GCF_018224955.1_ASM1822495v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:32,695] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:32,699] [INFO] DFAST_QC result json was written to GCF_018224955.1_ASM1822495v1_genomic.fna/dqc_result.json
[2024-01-25 18:14:32,699] [INFO] DFAST_QC completed!
[2024-01-25 18:14:32,699] [INFO] Total running time: 0h1m57s