[2023-06-17 14:48:38,934] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:48:38,936] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:48:38,936] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c144562-195d-4258-966e-08d3b7531aa8/dqc_reference
[2023-06-17 14:48:40,145] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:48:40,146] [INFO] Task started: Prodigal
[2023-06-17 14:48:40,146] [INFO] Running command: gunzip -c /var/lib/cwl/stg09cb56b8-9b64-4c9d-a756-13f92eccca2a/GCA_003501035.1_ASM350103v1_genomic.fna.gz | prodigal -d GCA_003501035.1_ASM350103v1_genomic.fna/cds.fna -a GCA_003501035.1_ASM350103v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:48:44,591] [INFO] Task succeeded: Prodigal
[2023-06-17 14:48:44,591] [INFO] Task started: HMMsearch
[2023-06-17 14:48:44,591] [INFO] Running command: hmmsearch --tblout GCA_003501035.1_ASM350103v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c144562-195d-4258-966e-08d3b7531aa8/dqc_reference/reference_markers.hmm GCA_003501035.1_ASM350103v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:48:44,754] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:48:44,755] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg09cb56b8-9b64-4c9d-a756-13f92eccca2a/GCA_003501035.1_ASM350103v1_genomic.fna.gz]
[2023-06-17 14:48:44,775] [INFO] Query marker FASTA was written to GCA_003501035.1_ASM350103v1_genomic.fna/markers.fasta
[2023-06-17 14:48:44,776] [INFO] Task started: Blastn
[2023-06-17 14:48:44,776] [INFO] Running command: blastn -query GCA_003501035.1_ASM350103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c144562-195d-4258-966e-08d3b7531aa8/dqc_reference/reference_markers.fasta -out GCA_003501035.1_ASM350103v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:48:45,429] [INFO] Task succeeded: Blastn
[2023-06-17 14:48:45,433] [INFO] Selected 19 target genomes.
[2023-06-17 14:48:45,433] [INFO] Target genome list was writen to GCA_003501035.1_ASM350103v1_genomic.fna/target_genomes.txt
[2023-06-17 14:48:45,435] [INFO] Task started: fastANI
[2023-06-17 14:48:45,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg09cb56b8-9b64-4c9d-a756-13f92eccca2a/GCA_003501035.1_ASM350103v1_genomic.fna.gz --refList GCA_003501035.1_ASM350103v1_genomic.fna/target_genomes.txt --output GCA_003501035.1_ASM350103v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:48:58,169] [INFO] Task succeeded: fastANI
[2023-06-17 14:48:58,170] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c144562-195d-4258-966e-08d3b7531aa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:48:58,170] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c144562-195d-4258-966e-08d3b7531aa8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:48:58,183] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:48:58,183] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 14:48:58,184] [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
Methyloceanibacter methanicus	strain=R-67174	GCA_001723285.1	1774968	1774968	type	True	86.7323	450	493	95	below_threshold
Methyloceanibacter stevinii	strain=R-67176	GCA_001723355.1	1774970	1774970	type	True	82.2726	435	493	95	below_threshold
Methyloceanibacter caenitepidi	strain=Gela4	GCA_000828475.1	1384459	1384459	type	True	81.8265	420	493	95	below_threshold
Methyloceanibacter marginalis	strain=R-67177	GCA_001723295.1	1774971	1774971	type	True	78.7435	216	493	95	below_threshold
Methyloceanibacter superfactus	strain=R-67175	GCA_001723305.1	1774969	1774969	type	True	78.2535	274	493	95	below_threshold
Methyloligella halotolerans	strain=VKM B-2706	GCA_001708935.1	1177755	1177755	type	True	77.1831	134	493	95	below_threshold
Parvibaculum indicum	strain=DSM 25305	GCA_011762095.1	562969	562969	type	True	76.7392	74	493	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.4813	61	493	95	below_threshold
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	76.4481	71	493	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.3926	62	493	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	76.2702	71	493	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	76.2033	62	493	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.152	69	493	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.1348	63	493	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	76.0458	73	493	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 14:48:58,186] [INFO] DFAST Taxonomy check result was written to GCA_003501035.1_ASM350103v1_genomic.fna/tc_result.tsv
[2023-06-17 14:48:58,186] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:48:58,186] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:48:58,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c144562-195d-4258-966e-08d3b7531aa8/dqc_reference/checkm_data
[2023-06-17 14:48:58,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:48:58,209] [INFO] Task started: CheckM
[2023-06-17 14:48:58,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003501035.1_ASM350103v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003501035.1_ASM350103v1_genomic.fna/checkm_input GCA_003501035.1_ASM350103v1_genomic.fna/checkm_result
[2023-06-17 14:49:16,455] [INFO] Task succeeded: CheckM
[2023-06-17 14:49:16,456] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:49:16,473] [INFO] ===== Completeness check finished =====
[2023-06-17 14:49:16,474] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:49:16,474] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003501035.1_ASM350103v1_genomic.fna/markers.fasta)
[2023-06-17 14:49:16,474] [INFO] Task started: Blastn
[2023-06-17 14:49:16,474] [INFO] Running command: blastn -query GCA_003501035.1_ASM350103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c144562-195d-4258-966e-08d3b7531aa8/dqc_reference/reference_markers_gtdb.fasta -out GCA_003501035.1_ASM350103v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:49:17,391] [INFO] Task succeeded: Blastn
[2023-06-17 14:49:17,422] [INFO] Selected 10 target genomes.
[2023-06-17 14:49:17,422] [INFO] Target genome list was writen to GCA_003501035.1_ASM350103v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:49:17,430] [INFO] Task started: fastANI
[2023-06-17 14:49:17,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg09cb56b8-9b64-4c9d-a756-13f92eccca2a/GCA_003501035.1_ASM350103v1_genomic.fna.gz --refList GCA_003501035.1_ASM350103v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003501035.1_ASM350103v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:49:23,962] [INFO] Task succeeded: fastANI
[2023-06-17 14:49:23,969] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 14:49:23,970] [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_001723285.1	s__Methyloceanibacter methanicus	86.7323	450	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001723355.1	s__Methyloceanibacter stevinii	82.2726	435	493	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	82.2492	431	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828475.1	s__Methyloceanibacter caenitepidi	81.8265	420	493	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	81.1545	377	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	98.85	98.85	0.80	0.80	2	-
GCF_001579845.1	s__Z2-YC6860 sp001579845	76.3662	71	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Z2-YC6860	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841195.1	s__Parvibaculum sp002841195	76.122	55	493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 14:49:23,972] [INFO] GTDB search result was written to GCA_003501035.1_ASM350103v1_genomic.fna/result_gtdb.tsv
[2023-06-17 14:49:23,972] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:49:23,976] [INFO] DFAST_QC result json was written to GCA_003501035.1_ASM350103v1_genomic.fna/dqc_result.json
[2023-06-17 14:49:23,976] [INFO] DFAST_QC completed!
[2023-06-17 14:49:23,976] [INFO] Total running time: 0h0m45s