[2023-06-29 12:42:48,870] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:42:48,873] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:42:48,873] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cee6a17-fe77-4d4b-adb3-1337f6339e69/dqc_reference
[2023-06-29 12:42:50,079] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:42:50,080] [INFO] Task started: Prodigal
[2023-06-29 12:42:50,080] [INFO] Running command: gunzip -c /var/lib/cwl/stg2248ee51-1a29-4459-8a0c-67c69e4e3713/GCA_023708165.1_ASM2370816v1_genomic.fna.gz | prodigal -d GCA_023708165.1_ASM2370816v1_genomic.fna/cds.fna -a GCA_023708165.1_ASM2370816v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:42:56,252] [INFO] Task succeeded: Prodigal
[2023-06-29 12:42:56,253] [INFO] Task started: HMMsearch
[2023-06-29 12:42:56,253] [INFO] Running command: hmmsearch --tblout GCA_023708165.1_ASM2370816v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cee6a17-fe77-4d4b-adb3-1337f6339e69/dqc_reference/reference_markers.hmm GCA_023708165.1_ASM2370816v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:42:56,481] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:42:56,482] [INFO] Found 6/6 markers.
[2023-06-29 12:42:56,506] [INFO] Query marker FASTA was written to GCA_023708165.1_ASM2370816v1_genomic.fna/markers.fasta
[2023-06-29 12:42:56,507] [INFO] Task started: Blastn
[2023-06-29 12:42:56,507] [INFO] Running command: blastn -query GCA_023708165.1_ASM2370816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cee6a17-fe77-4d4b-adb3-1337f6339e69/dqc_reference/reference_markers.fasta -out GCA_023708165.1_ASM2370816v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:42:57,084] [INFO] Task succeeded: Blastn
[2023-06-29 12:42:57,088] [INFO] Selected 18 target genomes.
[2023-06-29 12:42:57,088] [INFO] Target genome list was writen to GCA_023708165.1_ASM2370816v1_genomic.fna/target_genomes.txt
[2023-06-29 12:42:57,097] [INFO] Task started: fastANI
[2023-06-29 12:42:57,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg2248ee51-1a29-4459-8a0c-67c69e4e3713/GCA_023708165.1_ASM2370816v1_genomic.fna.gz --refList GCA_023708165.1_ASM2370816v1_genomic.fna/target_genomes.txt --output GCA_023708165.1_ASM2370816v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:43:03,945] [INFO] Task succeeded: fastANI
[2023-06-29 12:43:03,946] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cee6a17-fe77-4d4b-adb3-1337f6339e69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:43:03,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cee6a17-fe77-4d4b-adb3-1337f6339e69/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:43:03,954] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 12:43:03,954] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 12:43:03,955] [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
Acidaminococcus intestini	strain=DSM 21505	GCA_000425045.1	187327	187327	type	True	99.1565	626	720	95	conclusive
Acidaminococcus provencensis	strain=Marseille-P4266	GCA_900291475.1	2058289	2058289	type	True	77.7462	132	720	95	below_threshold
Acidaminococcus fermentans	strain=DSM 20731	GCA_000025305.1	905	905	type	True	77.6552	142	720	95	below_threshold
Acidaminococcus massiliensis	strain=Marseille-P2828	GCA_900095825.1	1852375	1852375	type	True	77.6359	133	720	95	below_threshold
Acidaminococcus timonensis	strain=Marseille-P2764	GCA_900106585.1	1871002	1871002	type	True	77.394	139	720	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:43:03,956] [INFO] DFAST Taxonomy check result was written to GCA_023708165.1_ASM2370816v1_genomic.fna/tc_result.tsv
[2023-06-29 12:43:03,957] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:43:03,957] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:43:03,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cee6a17-fe77-4d4b-adb3-1337f6339e69/dqc_reference/checkm_data
[2023-06-29 12:43:03,958] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:43:03,988] [INFO] Task started: CheckM
[2023-06-29 12:43:03,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708165.1_ASM2370816v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708165.1_ASM2370816v1_genomic.fna/checkm_input GCA_023708165.1_ASM2370816v1_genomic.fna/checkm_result
[2023-06-29 12:43:28,371] [INFO] Task succeeded: CheckM
[2023-06-29 12:43:28,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:43:28,394] [INFO] ===== Completeness check finished =====
[2023-06-29 12:43:28,394] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:43:28,394] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708165.1_ASM2370816v1_genomic.fna/markers.fasta)
[2023-06-29 12:43:28,395] [INFO] Task started: Blastn
[2023-06-29 12:43:28,395] [INFO] Running command: blastn -query GCA_023708165.1_ASM2370816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cee6a17-fe77-4d4b-adb3-1337f6339e69/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708165.1_ASM2370816v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:43:29,216] [INFO] Task succeeded: Blastn
[2023-06-29 12:43:29,221] [INFO] Selected 15 target genomes.
[2023-06-29 12:43:29,221] [INFO] Target genome list was writen to GCA_023708165.1_ASM2370816v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:43:29,247] [INFO] Task started: fastANI
[2023-06-29 12:43:29,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg2248ee51-1a29-4459-8a0c-67c69e4e3713/GCA_023708165.1_ASM2370816v1_genomic.fna.gz --refList GCA_023708165.1_ASM2370816v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708165.1_ASM2370816v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:43:35,422] [INFO] Task succeeded: fastANI
[2023-06-29 12:43:35,433] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:43:35,433] [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_000425045.1	s__Acidaminococcus intestini	99.1565	626	720	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	99.60	99.25	0.93	0.88	13	conclusive
GCA_900538365.1	s__Acidaminococcus sp900538365	92.0969	577	720	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	98.99	97.67	0.93	0.89	4	-
GCF_009696675.1	s__Acidaminococcus sp000437815	78.6884	139	720	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	98.16	97.76	0.92	0.89	4	-
GCA_902796945.1	s__Acidaminococcus sp902796945	78.1103	212	720	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315205.1	s__Acidaminococcus sp900315205	77.882	174	720	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	99.22	98.84	0.89	0.88	6	-
GCA_900770265.1	s__Acidaminococcus sp900770265	77.6734	94	720	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	96.61	96.61	0.81	0.81	2	-
GCF_000025305.1	s__Acidaminococcus fermentans	77.6487	143	720	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	98.69	98.27	0.92	0.87	11	-
GCF_900095825.1	s__Acidaminococcus massiliensis	77.6359	133	720	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	98.55	97.11	0.93	0.86	3	-
GCA_905215645.1	s__Acidaminococcus sp905215645	77.6064	126	720	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314165.1	s__Acidaminococcus sp900314165	77.3627	95	720	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Acidaminococcales;f__Acidaminococcaceae;g__Acidaminococcus	95.0	100.00	100.00	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-06-29 12:43:35,436] [INFO] GTDB search result was written to GCA_023708165.1_ASM2370816v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:43:35,436] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:43:35,441] [INFO] DFAST_QC result json was written to GCA_023708165.1_ASM2370816v1_genomic.fna/dqc_result.json
[2023-06-29 12:43:35,442] [INFO] DFAST_QC completed!
[2023-06-29 12:43:35,442] [INFO] Total running time: 0h0m47s