[2024-01-24 13:40:33,823] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:33,825] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:33,825] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1be4755-4e3a-4b59-880b-dc7c73794da7/dqc_reference
[2024-01-24 13:40:35,287] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:35,288] [INFO] Task started: Prodigal
[2024-01-24 13:40:35,288] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5357aa0-70c3-4ae1-af10-7a17d58707f9/GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna.gz | prodigal -d GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/cds.fna -a GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:44,777] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:44,777] [INFO] Task started: HMMsearch
[2024-01-24 13:40:44,778] [INFO] Running command: hmmsearch --tblout GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1be4755-4e3a-4b59-880b-dc7c73794da7/dqc_reference/reference_markers.hmm GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:45,056] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:45,057] [INFO] Found 6/6 markers.
[2024-01-24 13:40:45,087] [INFO] Query marker FASTA was written to GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/markers.fasta
[2024-01-24 13:40:45,087] [INFO] Task started: Blastn
[2024-01-24 13:40:45,087] [INFO] Running command: blastn -query GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1be4755-4e3a-4b59-880b-dc7c73794da7/dqc_reference/reference_markers.fasta -out GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:46,128] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:46,132] [INFO] Selected 20 target genomes.
[2024-01-24 13:40:46,132] [INFO] Target genome list was writen to GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/target_genomes.txt
[2024-01-24 13:40:46,162] [INFO] Task started: fastANI
[2024-01-24 13:40:46,162] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5357aa0-70c3-4ae1-af10-7a17d58707f9/GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna.gz --refList GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/target_genomes.txt --output GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:00,929] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:00,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1be4755-4e3a-4b59-880b-dc7c73794da7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:00,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1be4755-4e3a-4b59-880b-dc7c73794da7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:00,946] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:00,947] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:00,947] [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
Methyloligella halotolerans	strain=VKM B-2706	GCA_001708935.1	1177755	1177755	type	True	100.0	1051	1053	95	conclusive
Methyloceanibacter superfactus	strain=R-67175	GCA_001723305.1	1774969	1774969	type	True	78.1171	335	1053	95	below_threshold
Methyloceanibacter marginalis	strain=R-67177	GCA_001723295.1	1774971	1774971	type	True	78.0054	240	1053	95	below_threshold
Methyloceanibacter methanicus	strain=R-67174	GCA_001723285.1	1774968	1774968	type	True	77.8354	266	1053	95	below_threshold
Methyloceanibacter caenitepidi	strain=Gela4	GCA_000828475.1	1384459	1384459	type	True	77.7696	244	1053	95	below_threshold
Methyloceanibacter stevinii	strain=R-67176	GCA_001723355.1	1774970	1774970	type	True	77.4664	264	1053	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	77.268	182	1053	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	77.2352	204	1053	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.1856	182	1053	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	77.1758	158	1053	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	77.1055	166	1053	95	below_threshold
Dichotomicrobium thermohalophilum	strain=DSM 5002	GCA_003550175.1	933063	933063	type	True	77.0141	120	1053	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.9691	186	1053	95	below_threshold
Microvirga guangxiensis	strain=CGMCC 1.7666	GCA_900102135.1	549386	549386	type	True	76.9164	119	1053	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	76.7443	165	1053	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	76.7344	126	1053	95	below_threshold
Methylobacterium gossipiicola	strain=Gh-105	GCA_900113485.1	582675	582675	type	True	76.6834	142	1053	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	76.6096	155	1053	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	76.5545	121	1053	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	76.4134	99	1053	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:00,949] [INFO] DFAST Taxonomy check result was written to GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/tc_result.tsv
[2024-01-24 13:41:00,949] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:00,949] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:00,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1be4755-4e3a-4b59-880b-dc7c73794da7/dqc_reference/checkm_data
[2024-01-24 13:41:00,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:00,985] [INFO] Task started: CheckM
[2024-01-24 13:41:00,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/checkm_input GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/checkm_result
[2024-01-24 13:41:33,349] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:33,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:33,372] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:33,373] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:33,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/markers.fasta)
[2024-01-24 13:41:33,373] [INFO] Task started: Blastn
[2024-01-24 13:41:33,374] [INFO] Running command: blastn -query GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1be4755-4e3a-4b59-880b-dc7c73794da7/dqc_reference/reference_markers_gtdb.fasta -out GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:35,324] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:35,327] [INFO] Selected 18 target genomes.
[2024-01-24 13:41:35,327] [INFO] Target genome list was writen to GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:35,339] [INFO] Task started: fastANI
[2024-01-24 13:41:35,340] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5357aa0-70c3-4ae1-af10-7a17d58707f9/GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna.gz --refList GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/target_genomes_gtdb.txt --output GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:46,521] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:46,535] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:46,535] [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_001708935.1	s__Methyloligella halotolerans	100.0	1051	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloligella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013341275.1	s__Methyloligella sp013341275	80.1782	600	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloligella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001723305.1	s__Methyloceanibacter superfactus	78.1175	335	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001723295.1	s__Methyloceanibacter marginalis	77.9914	241	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001723285.1	s__Methyloceanibacter methanicus	77.8225	267	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482645.1	s__Methyloceanibacter sp002482645	77.8006	259	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	98.85	98.85	0.80	0.80	2	-
GCF_000828475.1	s__Methyloceanibacter caenitepidi	77.7562	245	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003071365.1	s__Methyloceanibacter sp003071365	77.6813	253	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380485.1	s__Methyloceanibacter sp014380485	77.5633	193	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016649675.1	s__Methyloceanibacter sp016649675	77.5596	236	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002383105.1	s__Methyloceanibacter sp002383105	77.5292	225	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	99.16	99.02	0.80	0.75	10	-
GCF_001723355.1	s__Methyloceanibacter stevinii	77.4778	263	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869535.1	s__Methyloceanibacter sp016869535	77.4282	228	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067145.1	s__Methyloceanibacter sp018067145	77.1696	178	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010525.1	s__Azorhizobium caulinodans	77.0906	167	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	97.54	97.54	0.94	0.94	2	-
GCF_900102135.1	s__Microvirga guangxiensis	76.9164	119	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422985.1	s__Methylobacterium sp001422985	76.7429	147	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.40	98.40	0.91	0.91	2	-
GCA_903885755.1	s__28-YEA-48 sp903885755	75.882	74	1053	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:46,537] [INFO] GTDB search result was written to GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:46,538] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:46,542] [INFO] DFAST_QC result json was written to GCF_001708935.1_Meth_hal_C2_1.0_genomic.fna/dqc_result.json
[2024-01-24 13:41:46,542] [INFO] DFAST_QC completed!
[2024-01-24 13:41:46,542] [INFO] Total running time: 0h1m13s