[2024-01-24 13:57:40,560] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:40,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:40,562] [INFO] DQC Reference Directory: /var/lib/cwl/stge53104a2-2958-44c9-9989-98aa0c573522/dqc_reference
[2024-01-24 13:57:41,891] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:41,892] [INFO] Task started: Prodigal
[2024-01-24 13:57:41,893] [INFO] Running command: gunzip -c /var/lib/cwl/stg26a38e1f-43c2-4c40-807f-2186f98137ec/GCF_005503535.1_ASM550353v1_genomic.fna.gz | prodigal -d GCF_005503535.1_ASM550353v1_genomic.fna/cds.fna -a GCF_005503535.1_ASM550353v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:04,568] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:04,568] [INFO] Task started: HMMsearch
[2024-01-24 13:58:04,569] [INFO] Running command: hmmsearch --tblout GCF_005503535.1_ASM550353v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge53104a2-2958-44c9-9989-98aa0c573522/dqc_reference/reference_markers.hmm GCF_005503535.1_ASM550353v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:04,857] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:04,858] [INFO] Found 6/6 markers.
[2024-01-24 13:58:04,914] [INFO] Query marker FASTA was written to GCF_005503535.1_ASM550353v1_genomic.fna/markers.fasta
[2024-01-24 13:58:04,915] [INFO] Task started: Blastn
[2024-01-24 13:58:04,915] [INFO] Running command: blastn -query GCF_005503535.1_ASM550353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge53104a2-2958-44c9-9989-98aa0c573522/dqc_reference/reference_markers.fasta -out GCF_005503535.1_ASM550353v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:05,982] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:05,985] [INFO] Selected 20 target genomes.
[2024-01-24 13:58:05,985] [INFO] Target genome list was writen to GCF_005503535.1_ASM550353v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:05,996] [INFO] Task started: fastANI
[2024-01-24 13:58:05,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg26a38e1f-43c2-4c40-807f-2186f98137ec/GCF_005503535.1_ASM550353v1_genomic.fna.gz --refList GCF_005503535.1_ASM550353v1_genomic.fna/target_genomes.txt --output GCF_005503535.1_ASM550353v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:41,210] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:41,211] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge53104a2-2958-44c9-9989-98aa0c573522/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:41,211] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge53104a2-2958-44c9-9989-98aa0c573522/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:41,232] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:41,232] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:41,232] [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
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	100.0	2415	2420	95	conclusive
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	87.6219	1579	2420	95	below_threshold
Mesorhizobium carmichaelinearum	strain=ICMP 18942	GCA_900199455.1	1208188	1208188	type	True	87.5688	1724	2420	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	87.4228	1573	2420	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	87.371	1619	2420	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	87.2314	1614	2420	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	87.1745	1416	2420	95	below_threshold
Mesorhizobium australicum	strain=WSM2073	GCA_000230995.3	536018	536018	type	True	87.022	1513	2420	95	below_threshold
Mesorhizobium norvegicum	strain=10.2.2	GCA_004919685.1	1085774	1085774	type	True	86.5081	1611	2420	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	86.2481	1524	2420	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	85.8174	1518	2420	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	84.7526	1400	2420	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	84.4008	1390	2420	95	below_threshold
Mesorhizobium hawassense	strain=AC99b	GCA_003289945.1	1209954	1209954	type	True	84.3194	1430	2420	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	84.2309	1218	2420	95	below_threshold
Mesorhizobium tamadayense	strain=DSM 28320	GCA_003863365.1	425306	425306	type	True	84.1561	1338	2420	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	83.9885	1247	2420	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.815	738	2420	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.7987	742	2420	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	78.7405	654	2420	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:41,247] [INFO] DFAST Taxonomy check result was written to GCF_005503535.1_ASM550353v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:41,248] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:41,248] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:41,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge53104a2-2958-44c9-9989-98aa0c573522/dqc_reference/checkm_data
[2024-01-24 13:58:41,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:41,338] [INFO] Task started: CheckM
[2024-01-24 13:58:41,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005503535.1_ASM550353v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005503535.1_ASM550353v1_genomic.fna/checkm_input GCF_005503535.1_ASM550353v1_genomic.fna/checkm_result
[2024-01-24 13:59:45,160] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:45,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:45,179] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:45,179] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:45,180] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005503535.1_ASM550353v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:45,180] [INFO] Task started: Blastn
[2024-01-24 13:59:45,180] [INFO] Running command: blastn -query GCF_005503535.1_ASM550353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge53104a2-2958-44c9-9989-98aa0c573522/dqc_reference/reference_markers_gtdb.fasta -out GCF_005503535.1_ASM550353v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:47,278] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:47,281] [INFO] Selected 23 target genomes.
[2024-01-24 13:59:47,282] [INFO] Target genome list was writen to GCF_005503535.1_ASM550353v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:47,306] [INFO] Task started: fastANI
[2024-01-24 13:59:47,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg26a38e1f-43c2-4c40-807f-2186f98137ec/GCF_005503535.1_ASM550353v1_genomic.fna.gz --refList GCF_005503535.1_ASM550353v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005503535.1_ASM550353v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:27,137] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:27,157] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:27,157] [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_005503535.1	s__Mesorhizobium sp005503535	100.0	2415	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017306585.1	s__Mesorhizobium sp017306585	90.6694	1757	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353565.1	s__Mesorhizobium sp003353565	87.9083	1699	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442315.1	s__Mesorhizobium sp006442315	87.7383	1745	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756495.1	s__Mesorhizobium sp016756495	87.7303	1659	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014189455.1	s__Mesorhizobium huakuii_A	87.6506	1713	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467435.1	s__Mesorhizobium sp016467435	87.5674	1540	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.58	98.58	0.95	0.95	2	-
GCF_900199455.1	s__Mesorhizobium carmichaelinearum	87.5627	1725	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013170825.1	s__Mesorhizobium sp013170825	87.5615	1637	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.36	95.35	0.82	0.81	3	-
GCF_013170705.1	s__Mesorhizobium loti_D	87.5554	1653	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.67	99.16	0.95	0.91	4	-
GCF_000688075.1	s__Mesorhizobium sp000688075	87.4881	1679	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009625.1	s__Mesorhizobium japonicum	87.401	1575	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.35	97.93	0.93	0.85	23	-
GCF_000472705.1	s__Mesorhizobium erdmanii	87.3745	1619	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.40	97.39	0.90	0.90	3	-
GCF_018588885.1	s__Mesorhizobium sp018588885	87.1703	1531	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013170805.1	s__Mesorhizobium sp013170805	87.1669	1603	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000472785.1	s__Mesorhizobium loti_E	87.0314	1673	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006658505.1	s__Mesorhizobium sp006658505	87.0277	1464	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.84	95.17	0.86	0.81	6	-
GCA_004791255.1	s__Mesorhizobium sp004791255	86.6996	1502	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.78	99.47	0.95	0.87	5	-
GCF_006442685.1	s__Mesorhizobium sp006442685	85.8564	1429	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.73	95.49	0.95	0.85	44	-
GCF_019091085.1	s__Mesorhizobium sp019091085	84.5442	1495	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000824785.1	s__Mesorhizobium plurifarium	84.4553	1476	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.23	96.62	0.87	0.84	6	-
GCA_001510895.1	s__Mesorhizobium loti_A	84.387	1379	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002295065.1	s__Mesorhizobium sp002295065	84.3161	1372	2420	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:27,163] [INFO] GTDB search result was written to GCF_005503535.1_ASM550353v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:27,163] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:27,168] [INFO] DFAST_QC result json was written to GCF_005503535.1_ASM550353v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:27,169] [INFO] DFAST_QC completed!
[2024-01-24 14:00:27,169] [INFO] Total running time: 0h2m47s