[2023-06-05 18:00:48,327] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:00:48,334] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:00:48,335] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f913bb1-af1a-4f31-9f55-474f94109307/dqc_reference
[2023-06-05 18:00:50,282] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:00:50,283] [INFO] Task started: Prodigal
[2023-06-05 18:00:50,283] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e116d9d-44dc-4f37-ba20-50cc27f131b1/GCA_934548045.1_ERR7738176_bin.74_genomic.fna.gz | prodigal -d GCA_934548045.1_ERR7738176_bin.74_genomic.fna/cds.fna -a GCA_934548045.1_ERR7738176_bin.74_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:00:57,265] [INFO] Task succeeded: Prodigal
[2023-06-05 18:00:57,265] [INFO] Task started: HMMsearch
[2023-06-05 18:00:57,265] [INFO] Running command: hmmsearch --tblout GCA_934548045.1_ERR7738176_bin.74_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f913bb1-af1a-4f31-9f55-474f94109307/dqc_reference/reference_markers.hmm GCA_934548045.1_ERR7738176_bin.74_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:00:57,560] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:00:57,562] [INFO] Found 6/6 markers.
[2023-06-05 18:00:57,600] [INFO] Query marker FASTA was written to GCA_934548045.1_ERR7738176_bin.74_genomic.fna/markers.fasta
[2023-06-05 18:00:57,601] [INFO] Task started: Blastn
[2023-06-05 18:00:57,601] [INFO] Running command: blastn -query GCA_934548045.1_ERR7738176_bin.74_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f913bb1-af1a-4f31-9f55-474f94109307/dqc_reference/reference_markers.fasta -out GCA_934548045.1_ERR7738176_bin.74_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:00:58,396] [INFO] Task succeeded: Blastn
[2023-06-05 18:00:58,400] [INFO] Selected 8 target genomes.
[2023-06-05 18:00:58,400] [INFO] Target genome list was writen to GCA_934548045.1_ERR7738176_bin.74_genomic.fna/target_genomes.txt
[2023-06-05 18:00:58,426] [INFO] Task started: fastANI
[2023-06-05 18:00:58,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e116d9d-44dc-4f37-ba20-50cc27f131b1/GCA_934548045.1_ERR7738176_bin.74_genomic.fna.gz --refList GCA_934548045.1_ERR7738176_bin.74_genomic.fna/target_genomes.txt --output GCA_934548045.1_ERR7738176_bin.74_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:01:02,767] [INFO] Task succeeded: fastANI
[2023-06-05 18:01:02,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f913bb1-af1a-4f31-9f55-474f94109307/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:01:02,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f913bb1-af1a-4f31-9f55-474f94109307/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:01:02,775] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:01:02,776] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:01:02,776] [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
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	83.0625	515	810	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	82.2217	482	810	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	82.1307	501	810	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	81.4481	445	810	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	79.9907	318	810	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:01:02,778] [INFO] DFAST Taxonomy check result was written to GCA_934548045.1_ERR7738176_bin.74_genomic.fna/tc_result.tsv
[2023-06-05 18:01:02,781] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:01:02,782] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:01:02,782] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f913bb1-af1a-4f31-9f55-474f94109307/dqc_reference/checkm_data
[2023-06-05 18:01:02,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:01:02,822] [INFO] Task started: CheckM
[2023-06-05 18:01:02,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934548045.1_ERR7738176_bin.74_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934548045.1_ERR7738176_bin.74_genomic.fna/checkm_input GCA_934548045.1_ERR7738176_bin.74_genomic.fna/checkm_result
[2023-06-05 18:01:30,076] [INFO] Task succeeded: CheckM
[2023-06-05 18:01:30,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:01:30,101] [INFO] ===== Completeness check finished =====
[2023-06-05 18:01:30,102] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:01:30,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934548045.1_ERR7738176_bin.74_genomic.fna/markers.fasta)
[2023-06-05 18:01:30,102] [INFO] Task started: Blastn
[2023-06-05 18:01:30,103] [INFO] Running command: blastn -query GCA_934548045.1_ERR7738176_bin.74_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f913bb1-af1a-4f31-9f55-474f94109307/dqc_reference/reference_markers_gtdb.fasta -out GCA_934548045.1_ERR7738176_bin.74_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:01:31,409] [INFO] Task succeeded: Blastn
[2023-06-05 18:01:31,433] [INFO] Selected 15 target genomes.
[2023-06-05 18:01:31,434] [INFO] Target genome list was writen to GCA_934548045.1_ERR7738176_bin.74_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:01:31,450] [INFO] Task started: fastANI
[2023-06-05 18:01:31,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e116d9d-44dc-4f37-ba20-50cc27f131b1/GCA_934548045.1_ERR7738176_bin.74_genomic.fna.gz --refList GCA_934548045.1_ERR7738176_bin.74_genomic.fna/target_genomes_gtdb.txt --output GCA_934548045.1_ERR7738176_bin.74_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:01:39,690] [INFO] Task succeeded: fastANI
[2023-06-05 18:01:39,704] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:01:39,704] [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_002549975.1	s__Faecalibacterium prausnitzii_H	83.1948	517	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.03	97.77	0.90	0.86	9	-
GCF_003293635.1	s__Faecalibacterium prausnitzii_G	83.177	506	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.11	95.97	0.86	0.76	34	-
GCF_002550035.1	s__Faecalibacterium prausnitzii_E	82.9872	527	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.41	96.74	0.87	0.80	12	-
GCA_900758465.1	s__Faecalibacterium sp900758465	82.8407	465	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.14	97.85	0.88	0.87	4	-
GCA_900551435.1	s__Faecalibacterium sp900551435	82.804	473	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.30	98.30	0.83	0.83	2	-
GCF_003287495.1	s__Faecalibacterium prausnitzii_I	82.2431	493	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.17	97.28	0.90	0.84	9	-
GCF_010509575.1	s__Faecalibacterium prausnitzii_C	82.1249	501	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.30	96.44	0.84	0.71	49	-
GCF_002549775.1	s__Faecalibacterium prausnitzii_F	82.0712	475	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.99	97.71	0.95	0.94	3	-
GCA_900539885.1	s__Faecalibacterium sp900539885	81.963	434	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.54	97.23	0.89	0.84	6	-
GCA_900539945.1	s__Faecalibacterium sp900539945	81.8289	446	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.71	98.00	0.92	0.86	4	-
GCF_003287405.1	s__Faecalibacterium prausnitzii_J	81.6255	459	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.32	96.98	0.87	0.83	5	-
GCA_002313795.1	s__Faecalibacterium prausnitzii_L	81.5706	358	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.80	98.80	0.73	0.73	2	-
GCA_014858325.1	s__Faecalibacterium sp014858325	81.4476	346	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003449675.1	s__Faecalibacterium sp003449675	81.132	320	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	96.56	96.55	0.80	0.74	3	-
GCA_900765105.1	s__Faecalibacterium sp900765105	80.9378	358	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.27	98.27	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-05 18:01:39,707] [INFO] GTDB search result was written to GCA_934548045.1_ERR7738176_bin.74_genomic.fna/result_gtdb.tsv
[2023-06-05 18:01:39,708] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:01:39,712] [INFO] DFAST_QC result json was written to GCA_934548045.1_ERR7738176_bin.74_genomic.fna/dqc_result.json
[2023-06-05 18:01:39,712] [INFO] DFAST_QC completed!
[2023-06-05 18:01:39,712] [INFO] Total running time: 0h0m51s