[2024-01-24 12:52:26,696] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:26,699] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:26,699] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ca9f58a-8777-4467-b9d6-b398d77a9326/dqc_reference
[2024-01-24 12:52:27,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:27,955] [INFO] Task started: Prodigal
[2024-01-24 12:52:27,955] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8b6e5e0-443b-429c-b17b-ac1a8453cd79/GCF_014218335.1_ASM1421833v1_genomic.fna.gz | prodigal -d GCF_014218335.1_ASM1421833v1_genomic.fna/cds.fna -a GCF_014218335.1_ASM1421833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:38,957] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:38,958] [INFO] Task started: HMMsearch
[2024-01-24 12:52:38,958] [INFO] Running command: hmmsearch --tblout GCF_014218335.1_ASM1421833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ca9f58a-8777-4467-b9d6-b398d77a9326/dqc_reference/reference_markers.hmm GCF_014218335.1_ASM1421833v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:39,298] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:39,300] [INFO] Found 6/6 markers.
[2024-01-24 12:52:39,350] [INFO] Query marker FASTA was written to GCF_014218335.1_ASM1421833v1_genomic.fna/markers.fasta
[2024-01-24 12:52:39,351] [INFO] Task started: Blastn
[2024-01-24 12:52:39,351] [INFO] Running command: blastn -query GCF_014218335.1_ASM1421833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ca9f58a-8777-4467-b9d6-b398d77a9326/dqc_reference/reference_markers.fasta -out GCF_014218335.1_ASM1421833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:40,011] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:40,016] [INFO] Selected 20 target genomes.
[2024-01-24 12:52:40,016] [INFO] Target genome list was writen to GCF_014218335.1_ASM1421833v1_genomic.fna/target_genomes.txt
[2024-01-24 12:52:40,029] [INFO] Task started: fastANI
[2024-01-24 12:52:40,029] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8b6e5e0-443b-429c-b17b-ac1a8453cd79/GCF_014218335.1_ASM1421833v1_genomic.fna.gz --refList GCF_014218335.1_ASM1421833v1_genomic.fna/target_genomes.txt --output GCF_014218335.1_ASM1421833v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:52:56,096] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:56,097] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ca9f58a-8777-4467-b9d6-b398d77a9326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:52:56,097] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ca9f58a-8777-4467-b9d6-b398d77a9326/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:52:56,106] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:52:56,107] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:52:56,107] [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
Anaerocolumna cellulosilytica	strain=SN021	GCA_014218335.1	433286	433286	type	True	100.0	1810	1810	95	conclusive
Anaerocolumna cellulosilytica	strain=DSM 100423	GCA_014202875.1	433286	433286	type	True	99.9565	1746	1810	95	conclusive
Anaerocolumna sedimenticola	strain=CBA3638	GCA_009931695.1	2696063	2696063	type	True	78.6772	283	1810	95	below_threshold
Anaerocolumna chitinilytica	strain=CTTW	GCA_014218355.1	1727145	1727145	type	True	78.3113	223	1810	95	below_threshold
Anaerocolumna aminovalerica	strain=DSM 1283	GCA_900115365.1	1527	1527	type	True	78.0315	188	1810	95	below_threshold
Anaerocolumna jejuensis	strain=DSM 15929	GCA_900142215.1	259063	259063	type	True	77.8531	232	1810	95	below_threshold
Mobilisporobacter senegalensis	strain=DSM 26537	GCA_003752155.1	1329262	1329262	type	True	77.6379	105	1810	95	below_threshold
Anaerosporobacter mobilis	strain=DSM 15930	GCA_900142955.1	264463	264463	type	True	77.4781	96	1810	95	below_threshold
Anaerocolumna xylanovorans	strain=DSM 12503	GCA_900143645.1	100134	100134	type	True	77.4474	212	1810	95	below_threshold
Mobilitalea sibirica	strain=DSM 26468	GCA_015999265.1	1462919	1462919	type	True	76.8954	100	1810	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:52:56,115] [INFO] DFAST Taxonomy check result was written to GCF_014218335.1_ASM1421833v1_genomic.fna/tc_result.tsv
[2024-01-24 12:52:56,116] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:52:56,116] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:52:56,116] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ca9f58a-8777-4467-b9d6-b398d77a9326/dqc_reference/checkm_data
[2024-01-24 12:52:56,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:52:56,170] [INFO] Task started: CheckM
[2024-01-24 12:52:56,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014218335.1_ASM1421833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014218335.1_ASM1421833v1_genomic.fna/checkm_input GCF_014218335.1_ASM1421833v1_genomic.fna/checkm_result
[2024-01-24 12:53:32,455] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:32,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:32,482] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:32,483] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:32,483] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014218335.1_ASM1421833v1_genomic.fna/markers.fasta)
[2024-01-24 12:53:32,483] [INFO] Task started: Blastn
[2024-01-24 12:53:32,484] [INFO] Running command: blastn -query GCF_014218335.1_ASM1421833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ca9f58a-8777-4467-b9d6-b398d77a9326/dqc_reference/reference_markers_gtdb.fasta -out GCF_014218335.1_ASM1421833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:33,460] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:33,465] [INFO] Selected 19 target genomes.
[2024-01-24 12:53:33,465] [INFO] Target genome list was writen to GCF_014218335.1_ASM1421833v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:33,506] [INFO] Task started: fastANI
[2024-01-24 12:53:33,506] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8b6e5e0-443b-429c-b17b-ac1a8453cd79/GCF_014218335.1_ASM1421833v1_genomic.fna.gz --refList GCF_014218335.1_ASM1421833v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014218335.1_ASM1421833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:47,487] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:47,500] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:47,501] [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_014218335.1	s__Anaerocolumna cellulosilytica	100.0	1810	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000702945.1	s__Anaerocolumna sp000702945	78.8202	255	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009931695.1	s__Anaerocolumna sedimenticola	78.6624	284	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016591975.1	s__TB5 sp016591975	78.5927	120	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__TB5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218355.1	s__Anaerocolumna sp014218355	78.263	221	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434335.1	s__Anaerocolumna sp002434335	78.166	225	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	99.22	99.22	0.91	0.91	2	-
GCF_900115365.1	s__Anaerocolumna aminovalerica	78.0315	188	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	99.17	99.14	0.90	0.89	3	-
GCF_900142215.1	s__Anaerocolumna jejuensis	77.8425	231	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752155.1	s__Mobilisporobacter senegalensis	77.6379	105	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilisporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142955.1	s__Anaerosporobacter mobilis	77.545	95	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerosporobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143645.1	s__Anaerocolumna xylanovorans	77.447	212	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655075.1	s__Anaerocolumna sp015655075	77.1375	149	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655565.1	s__Anaerocolumna sp015655565	77.1124	127	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerocolumna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940225.1	s__14-2 sp001940225	77.0331	51	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002419585.1	s__Velocimicrobium sp002419585	76.8617	80	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Velocimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012839085.1	s__Mobilitalea sp012839085	76.6229	59	1810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mobilitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:53:47,503] [INFO] GTDB search result was written to GCF_014218335.1_ASM1421833v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:47,503] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:47,509] [INFO] DFAST_QC result json was written to GCF_014218335.1_ASM1421833v1_genomic.fna/dqc_result.json
[2024-01-24 12:53:47,510] [INFO] DFAST_QC completed!
[2024-01-24 12:53:47,510] [INFO] Total running time: 0h1m21s