[2023-06-30 03:00:35,008] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:00:35,011] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:00:35,012] [INFO] DQC Reference Directory: /var/lib/cwl/stg3464feaa-b98e-4212-8f2a-e555398700c3/dqc_reference
[2023-06-30 03:00:36,287] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:00:36,288] [INFO] Task started: Prodigal
[2023-06-30 03:00:36,288] [INFO] Running command: gunzip -c /var/lib/cwl/stg30c4f1f8-c872-4cdd-8146-73b7296f59cb/GCA_024280355.1_ASM2428035v1_genomic.fna.gz | prodigal -d GCA_024280355.1_ASM2428035v1_genomic.fna/cds.fna -a GCA_024280355.1_ASM2428035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:00:42,116] [INFO] Task succeeded: Prodigal
[2023-06-30 03:00:42,116] [INFO] Task started: HMMsearch
[2023-06-30 03:00:42,117] [INFO] Running command: hmmsearch --tblout GCA_024280355.1_ASM2428035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3464feaa-b98e-4212-8f2a-e555398700c3/dqc_reference/reference_markers.hmm GCA_024280355.1_ASM2428035v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:00:42,388] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:00:42,390] [INFO] Found 6/6 markers.
[2023-06-30 03:00:42,427] [INFO] Query marker FASTA was written to GCA_024280355.1_ASM2428035v1_genomic.fna/markers.fasta
[2023-06-30 03:00:42,428] [INFO] Task started: Blastn
[2023-06-30 03:00:42,428] [INFO] Running command: blastn -query GCA_024280355.1_ASM2428035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3464feaa-b98e-4212-8f2a-e555398700c3/dqc_reference/reference_markers.fasta -out GCA_024280355.1_ASM2428035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:00:43,060] [INFO] Task succeeded: Blastn
[2023-06-30 03:00:43,084] [INFO] Selected 33 target genomes.
[2023-06-30 03:00:43,085] [INFO] Target genome list was writen to GCA_024280355.1_ASM2428035v1_genomic.fna/target_genomes.txt
[2023-06-30 03:00:43,089] [INFO] Task started: fastANI
[2023-06-30 03:00:43,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg30c4f1f8-c872-4cdd-8146-73b7296f59cb/GCA_024280355.1_ASM2428035v1_genomic.fna.gz --refList GCA_024280355.1_ASM2428035v1_genomic.fna/target_genomes.txt --output GCA_024280355.1_ASM2428035v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:01:07,672] [INFO] Task succeeded: fastANI
[2023-06-30 03:01:07,673] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3464feaa-b98e-4212-8f2a-e555398700c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:01:07,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3464feaa-b98e-4212-8f2a-e555398700c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:01:07,679] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:01:07,679] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:01:07,680] [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
Methyloprofundus sedimenti	strain=WF1	GCA_002072955.1	1420851	1420851	type	True	76.6514	80	1064	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:01:07,682] [INFO] DFAST Taxonomy check result was written to GCA_024280355.1_ASM2428035v1_genomic.fna/tc_result.tsv
[2023-06-30 03:01:07,682] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:01:07,683] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:01:07,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3464feaa-b98e-4212-8f2a-e555398700c3/dqc_reference/checkm_data
[2023-06-30 03:01:07,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:01:07,725] [INFO] Task started: CheckM
[2023-06-30 03:01:07,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024280355.1_ASM2428035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024280355.1_ASM2428035v1_genomic.fna/checkm_input GCA_024280355.1_ASM2428035v1_genomic.fna/checkm_result
[2023-06-30 03:01:31,963] [INFO] Task succeeded: CheckM
[2023-06-30 03:01:31,965] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:01:31,986] [INFO] ===== Completeness check finished =====
[2023-06-30 03:01:31,986] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:01:31,987] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024280355.1_ASM2428035v1_genomic.fna/markers.fasta)
[2023-06-30 03:01:31,987] [INFO] Task started: Blastn
[2023-06-30 03:01:31,987] [INFO] Running command: blastn -query GCA_024280355.1_ASM2428035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3464feaa-b98e-4212-8f2a-e555398700c3/dqc_reference/reference_markers_gtdb.fasta -out GCA_024280355.1_ASM2428035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:01:32,955] [INFO] Task succeeded: Blastn
[2023-06-30 03:01:32,960] [INFO] Selected 25 target genomes.
[2023-06-30 03:01:32,960] [INFO] Target genome list was writen to GCA_024280355.1_ASM2428035v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:01:32,964] [INFO] Task started: fastANI
[2023-06-30 03:01:32,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg30c4f1f8-c872-4cdd-8146-73b7296f59cb/GCA_024280355.1_ASM2428035v1_genomic.fna.gz --refList GCA_024280355.1_ASM2428035v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024280355.1_ASM2428035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:01:44,467] [INFO] Task succeeded: fastANI
[2023-06-30 03:01:44,480] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 03:01:44,480] [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_003666385.1	s__QPIN01 sp003666385	77.0282	124	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__QPIN01	95.0	99.51	99.51	0.97	0.97	2	-
GCA_003666325.1	s__QPIN01 sp003666325	76.8244	126	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__QPIN01	95.0	99.86	99.86	0.96	0.96	2	-
GCA_013139755.1	s__QPIN01 sp013139755	76.6636	173	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__QPIN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002072955.1	s__Methyloprofundus sedimenti	76.6264	82	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128525.1	s__Methyloprofundus sp900128525	76.4251	68	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138855.1	s__WTBX01 sp013138855	76.2741	58	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__WTBX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917345.1	s__KS41 sp903917345	76.2093	51	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.26	98.86	0.95	0.89	10	-
GCA_016592635.1	s__Methyloprofundus sp016592635	76.1548	67	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methyloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934035.1	s__KS41 sp903934035	75.8573	53	1064	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.03	98.98	0.89	0.84	3	-
--------------------------------------------------------------------------------
[2023-06-30 03:01:44,482] [INFO] GTDB search result was written to GCA_024280355.1_ASM2428035v1_genomic.fna/result_gtdb.tsv
[2023-06-30 03:01:44,483] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:01:44,486] [INFO] DFAST_QC result json was written to GCA_024280355.1_ASM2428035v1_genomic.fna/dqc_result.json
[2023-06-30 03:01:44,486] [INFO] DFAST_QC completed!
[2023-06-30 03:01:44,486] [INFO] Total running time: 0h1m9s