[2024-01-24 13:01:24,830] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:24,832] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:24,832] [INFO] DQC Reference Directory: /var/lib/cwl/stg13a1a3e4-da41-4cea-84f2-c5d42b7c6f24/dqc_reference
[2024-01-24 13:01:26,268] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:26,269] [INFO] Task started: Prodigal
[2024-01-24 13:01:26,269] [INFO] Running command: gunzip -c /var/lib/cwl/stg39ac7849-7fda-4958-a2b2-349790b72bdb/GCF_900290205.1_PRJEB22816_genomic.fna.gz | prodigal -d GCF_900290205.1_PRJEB22816_genomic.fna/cds.fna -a GCF_900290205.1_PRJEB22816_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:35,306] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:35,306] [INFO] Task started: HMMsearch
[2024-01-24 13:01:35,306] [INFO] Running command: hmmsearch --tblout GCF_900290205.1_PRJEB22816_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13a1a3e4-da41-4cea-84f2-c5d42b7c6f24/dqc_reference/reference_markers.hmm GCF_900290205.1_PRJEB22816_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:35,576] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:35,577] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg39ac7849-7fda-4958-a2b2-349790b72bdb/GCF_900290205.1_PRJEB22816_genomic.fna.gz]
[2024-01-24 13:01:35,631] [INFO] Query marker FASTA was written to GCF_900290205.1_PRJEB22816_genomic.fna/markers.fasta
[2024-01-24 13:01:35,632] [INFO] Task started: Blastn
[2024-01-24 13:01:35,632] [INFO] Running command: blastn -query GCF_900290205.1_PRJEB22816_genomic.fna/markers.fasta -db /var/lib/cwl/stg13a1a3e4-da41-4cea-84f2-c5d42b7c6f24/dqc_reference/reference_markers.fasta -out GCF_900290205.1_PRJEB22816_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:36,293] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:36,460] [INFO] Selected 25 target genomes.
[2024-01-24 13:01:36,461] [INFO] Target genome list was writen to GCF_900290205.1_PRJEB22816_genomic.fna/target_genomes.txt
[2024-01-24 13:01:36,480] [INFO] Task started: fastANI
[2024-01-24 13:01:36,480] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ac7849-7fda-4958-a2b2-349790b72bdb/GCF_900290205.1_PRJEB22816_genomic.fna.gz --refList GCF_900290205.1_PRJEB22816_genomic.fna/target_genomes.txt --output GCF_900290205.1_PRJEB22816_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:51,941] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:51,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13a1a3e4-da41-4cea-84f2-c5d42b7c6f24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:51,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13a1a3e4-da41-4cea-84f2-c5d42b7c6f24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:51,946] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:01:51,946] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:01:51,947] [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
Galactobacillus timonensis	strain=Marseille-P4641	GCA_900240265.1	2041840	2041840	type	True	82.1667	238	1099	95	below_threshold
Lactimicrobium massiliense	strain=Marseille-P4301	GCA_900343155.1	2161814	2161814	type	True	78.628	135	1099	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:51,948] [INFO] DFAST Taxonomy check result was written to GCF_900290205.1_PRJEB22816_genomic.fna/tc_result.tsv
[2024-01-24 13:01:51,949] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:51,949] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:51,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13a1a3e4-da41-4cea-84f2-c5d42b7c6f24/dqc_reference/checkm_data
[2024-01-24 13:01:51,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:51,985] [INFO] Task started: CheckM
[2024-01-24 13:01:51,986] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900290205.1_PRJEB22816_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900290205.1_PRJEB22816_genomic.fna/checkm_input GCF_900290205.1_PRJEB22816_genomic.fna/checkm_result
[2024-01-24 13:02:24,070] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:24,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:24,096] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:24,096] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:24,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900290205.1_PRJEB22816_genomic.fna/markers.fasta)
[2024-01-24 13:02:24,097] [INFO] Task started: Blastn
[2024-01-24 13:02:24,097] [INFO] Running command: blastn -query GCF_900290205.1_PRJEB22816_genomic.fna/markers.fasta -db /var/lib/cwl/stg13a1a3e4-da41-4cea-84f2-c5d42b7c6f24/dqc_reference/reference_markers_gtdb.fasta -out GCF_900290205.1_PRJEB22816_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:25,004] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:25,007] [INFO] Selected 18 target genomes.
[2024-01-24 13:02:25,008] [INFO] Target genome list was writen to GCF_900290205.1_PRJEB22816_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:25,043] [INFO] Task started: fastANI
[2024-01-24 13:02:25,043] [INFO] Running command: fastANI --query /var/lib/cwl/stg39ac7849-7fda-4958-a2b2-349790b72bdb/GCF_900290205.1_PRJEB22816_genomic.fna.gz --refList GCF_900290205.1_PRJEB22816_genomic.fna/target_genomes_gtdb.txt --output GCF_900290205.1_PRJEB22816_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:33,457] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:33,469] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:33,469] [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_009696165.1	s__Bulleidia intestinalis	97.175	809	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.55	97.14	0.90	0.85	19	conclusive
GCA_900314905.1	s__Bulleidia sp900314905	88.8835	622	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.98	99.98	0.96	0.96	2	-
GCA_900770275.1	s__Bulleidia sp900770275	78.2469	140	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314345.1	s__Bulleidia sp900314345	78.1272	139	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	100.00	100.00	0.98	0.98	2	-
GCA_017512725.1	s__Bulleidia sp017512725	77.3895	107	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017433125.1	s__Bulleidia sp017433125	77.3221	66	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.54	98.45	0.90	0.88	3	-
GCA_017469885.1	s__Bulleidia sp017469885	77.2289	114	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761625.1	s__Bulleidia sp902761625	77.2143	68	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902786245.1	s__Bulleidia sp902786245	77.1557	106	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015058875.1	s__Bulleidia sp015058875	77.1262	104	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	97.73	97.73	0.82	0.82	2	-
GCA_016280695.1	s__Bulleidia sp016280695	77.0332	52	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017420585.1	s__Bulleidia sp017420585	77.0159	59	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.75	98.73	0.84	0.83	3	-
GCA_902775735.1	s__Bulleidia sp902775735	76.8165	59	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.20	97.93	0.87	0.80	4	-
GCA_905235315.1	s__Bulleidia sp905235315	76.743	82	1099	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:33,472] [INFO] GTDB search result was written to GCF_900290205.1_PRJEB22816_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:33,472] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:33,475] [INFO] DFAST_QC result json was written to GCF_900290205.1_PRJEB22816_genomic.fna/dqc_result.json
[2024-01-24 13:02:33,475] [INFO] DFAST_QC completed!
[2024-01-24 13:02:33,475] [INFO] Total running time: 0h1m9s