[2024-01-25 19:40:05,524] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:40:05,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:40:05,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg08dc3789-470c-49f4-8329-e11c92817142/dqc_reference
[2024-01-25 19:40:06,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:40:06,646] [INFO] Task started: Prodigal
[2024-01-25 19:40:06,646] [INFO] Running command: gunzip -c /var/lib/cwl/stg39b9a923-6e49-423a-8ecf-cfc752e2064d/GCF_024160205.1_ASM2416020v1_genomic.fna.gz | prodigal -d GCF_024160205.1_ASM2416020v1_genomic.fna/cds.fna -a GCF_024160205.1_ASM2416020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:40:13,036] [INFO] Task succeeded: Prodigal
[2024-01-25 19:40:13,036] [INFO] Task started: HMMsearch
[2024-01-25 19:40:13,036] [INFO] Running command: hmmsearch --tblout GCF_024160205.1_ASM2416020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08dc3789-470c-49f4-8329-e11c92817142/dqc_reference/reference_markers.hmm GCF_024160205.1_ASM2416020v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:40:13,264] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:40:13,265] [INFO] Found 6/6 markers.
[2024-01-25 19:40:13,295] [INFO] Query marker FASTA was written to GCF_024160205.1_ASM2416020v1_genomic.fna/markers.fasta
[2024-01-25 19:40:13,295] [INFO] Task started: Blastn
[2024-01-25 19:40:13,295] [INFO] Running command: blastn -query GCF_024160205.1_ASM2416020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08dc3789-470c-49f4-8329-e11c92817142/dqc_reference/reference_markers.fasta -out GCF_024160205.1_ASM2416020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:13,902] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:13,905] [INFO] Selected 22 target genomes.
[2024-01-25 19:40:13,905] [INFO] Target genome list was writen to GCF_024160205.1_ASM2416020v1_genomic.fna/target_genomes.txt
[2024-01-25 19:40:13,914] [INFO] Task started: fastANI
[2024-01-25 19:40:13,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg39b9a923-6e49-423a-8ecf-cfc752e2064d/GCF_024160205.1_ASM2416020v1_genomic.fna.gz --refList GCF_024160205.1_ASM2416020v1_genomic.fna/target_genomes.txt --output GCF_024160205.1_ASM2416020v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:40:26,446] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:26,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08dc3789-470c-49f4-8329-e11c92817142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:40:26,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08dc3789-470c-49f4-8329-e11c92817142/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:40:26,455] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:40:26,455] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:40:26,455] [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
Aequitasia blattaphilus	strain=PAL113	GCA_024160205.1	2949332	2949332	type	True	100.0	1030	1038	95	conclusive
Aequitasia blattaphilus	strain=PAL113	GCA_024721305.1	2949332	2949332	type	True	100.0	1030	1038	95	conclusive
Ohessyouella blattaphilus	strain=PAL227	GCA_024160185.1	2949333	2949333	type	True	82.7597	116	1038	95	below_threshold
Ohessyouella blattaphilus	strain=PAL227	GCA_024721265.1	2949333	2949333	type	True	82.7597	116	1038	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	79.0104	71	1038	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	78.8868	69	1038	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	78.4389	65	1038	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	78.4075	55	1038	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	78.3787	64	1038	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	78.304	62	1038	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	77.629	77	1038	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	77.4339	51	1038	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:40:26,457] [INFO] DFAST Taxonomy check result was written to GCF_024160205.1_ASM2416020v1_genomic.fna/tc_result.tsv
[2024-01-25 19:40:26,457] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:40:26,457] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:40:26,458] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08dc3789-470c-49f4-8329-e11c92817142/dqc_reference/checkm_data
[2024-01-25 19:40:26,458] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:40:26,493] [INFO] Task started: CheckM
[2024-01-25 19:40:26,493] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024160205.1_ASM2416020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024160205.1_ASM2416020v1_genomic.fna/checkm_input GCF_024160205.1_ASM2416020v1_genomic.fna/checkm_result
[2024-01-25 19:40:50,499] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:50,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:50,520] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:50,520] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:50,520] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024160205.1_ASM2416020v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:50,520] [INFO] Task started: Blastn
[2024-01-25 19:40:50,521] [INFO] Running command: blastn -query GCF_024160205.1_ASM2416020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08dc3789-470c-49f4-8329-e11c92817142/dqc_reference/reference_markers_gtdb.fasta -out GCF_024160205.1_ASM2416020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:51,532] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:51,535] [INFO] Selected 34 target genomes.
[2024-01-25 19:40:51,535] [INFO] Target genome list was writen to GCF_024160205.1_ASM2416020v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:51,555] [INFO] Task started: fastANI
[2024-01-25 19:40:51,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg39b9a923-6e49-423a-8ecf-cfc752e2064d/GCF_024160205.1_ASM2416020v1_genomic.fna.gz --refList GCF_024160205.1_ASM2416020v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024160205.1_ASM2416020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:41:07,471] [INFO] Task succeeded: fastANI
[2024-01-25 19:41:07,481] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:41:07,482] [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_004295125.1	s__Clostridium_AP scindens	78.9513	61	1038	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AP	95.0	99.44	99.12	0.90	0.78	13	-
GCF_000154065.1	s__Dorea_A longicatena	78.8868	69	1038	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	98.55	97.61	0.85	0.69	49	-
GCF_000169235.1	s__Dorea formicigenerans	78.6119	62	1038	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea	95.0	97.68	96.97	0.80	0.73	43	-
GCF_004346095.1	s__Faecalimonas umbilicata	78.3948	54	1038	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	98.30	97.78	0.83	0.78	20	-
GCF_008121495.1	s__Ruminococcus_B gnavus	78.3684	63	1038	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	98.58	96.13	0.80	0.66	102	-
GCF_001404875.1	s__Dorea_A longicatena_B	78.2304	71	1038	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	97.75	96.72	0.80	0.69	20	-
GCA_902381685.1	s__Faecalimonas sp000209385	78.1096	51	1038	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	99.49	98.98	0.93	0.86	3	-
GCF_900240315.1	s__Dorea_B phocaeensis	77.633	76	1038	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_B	95.0	98.22	97.28	0.87	0.81	8	-
GCA_018883985.1	s__Ruminococcus_B intestinipullorum	77.312	61	1038	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000155875.1	s__Bariatricus comes	77.2179	61	1038	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	-
GCA_019113475.1	s__Suipraeoptans intestinavium	76.9283	64	1038	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Suipraeoptans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287475.1	s__Mediterraneibacter sp014287475	76.8538	55	1038	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.03	96.03	0.75	0.75	2	-
GCA_003481745.1	s__Blautia stercoris	76.8124	50	1038	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.69	97.83	0.91	0.84	8	-
GCA_017465565.1	s__Faecalimonas sp017465565	76.6817	57	1038	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905203555.1	s__Schaedlerella sp905203555	76.1467	62	1038	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:41:07,483] [INFO] GTDB search result was written to GCF_024160205.1_ASM2416020v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:41:07,484] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:41:07,486] [INFO] DFAST_QC result json was written to GCF_024160205.1_ASM2416020v1_genomic.fna/dqc_result.json
[2024-01-25 19:41:07,487] [INFO] DFAST_QC completed!
[2024-01-25 19:41:07,487] [INFO] Total running time: 0h1m2s