[2024-01-24 11:12:24,423] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:24,426] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:24,426] [INFO] DQC Reference Directory: /var/lib/cwl/stg234b814c-434f-400d-8733-3497a2a026b8/dqc_reference
[2024-01-24 11:12:27,086] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:27,093] [INFO] Task started: Prodigal
[2024-01-24 11:12:27,094] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd65c54b-1126-4c5c-9d6e-3ba8264b1467/GCF_014287955.1_ASM1428795v1_genomic.fna.gz | prodigal -d GCF_014287955.1_ASM1428795v1_genomic.fna/cds.fna -a GCF_014287955.1_ASM1428795v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:33,540] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:33,541] [INFO] Task started: HMMsearch
[2024-01-24 11:12:33,541] [INFO] Running command: hmmsearch --tblout GCF_014287955.1_ASM1428795v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg234b814c-434f-400d-8733-3497a2a026b8/dqc_reference/reference_markers.hmm GCF_014287955.1_ASM1428795v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:33,869] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:33,870] [INFO] Found 6/6 markers.
[2024-01-24 11:12:33,899] [INFO] Query marker FASTA was written to GCF_014287955.1_ASM1428795v1_genomic.fna/markers.fasta
[2024-01-24 11:12:33,899] [INFO] Task started: Blastn
[2024-01-24 11:12:33,899] [INFO] Running command: blastn -query GCF_014287955.1_ASM1428795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg234b814c-434f-400d-8733-3497a2a026b8/dqc_reference/reference_markers.fasta -out GCF_014287955.1_ASM1428795v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:34,572] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:34,577] [INFO] Selected 24 target genomes.
[2024-01-24 11:12:34,578] [INFO] Target genome list was writen to GCF_014287955.1_ASM1428795v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:34,588] [INFO] Task started: fastANI
[2024-01-24 11:12:34,589] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd65c54b-1126-4c5c-9d6e-3ba8264b1467/GCF_014287955.1_ASM1428795v1_genomic.fna.gz --refList GCF_014287955.1_ASM1428795v1_genomic.fna/target_genomes.txt --output GCF_014287955.1_ASM1428795v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:47,768] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:47,768] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg234b814c-434f-400d-8733-3497a2a026b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:47,768] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg234b814c-434f-400d-8733-3497a2a026b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:47,787] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:12:47,787] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:12:47,788] [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
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	82.4049	59	963	95	below_threshold
Jutongia hominis	strain=BX3	GCA_014384965.1	2763664	2763664	type	True	82.3056	83	963	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	80.5888	69	963	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	80.4666	285	963	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_025149915.1	33043	33043	suspected-type	True	80.2336	74	963	95	below_threshold
Butyrivibrio crossotus	strain=DSM 2876	GCA_000156015.1	45851	45851	type	True	80.105	121	963	95	below_threshold
Butyrivibrio crossotus	strain=DSM 2876	GCA_025148445.1	45851	45851	type	True	80.0963	124	963	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_000153885.1	39496	39496	suspected-type	True	79.8043	90	963	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	79.5947	89	963	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	78.422	77	963	95	below_threshold
Lachnospira multipara	strain=ATCC 19207	GCA_000424105.1	28051	28051	type	True	78.0041	114	963	95	below_threshold
Anaerostipes faecalis	strain=AGMB03513	GCA_018982945.1	2738446	2738446	type	True	77.3192	50	963	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	76.8937	56	963	95	below_threshold
Butyrivibrio hungatei	strain=DSM 14810	GCA_900143205.1	185008	185008	type	True	76.7807	51	963	95	below_threshold
Acetitomaculum ruminis	strain=DSM 5522	GCA_900112085.1	2382	2382	type	True	76.6575	52	963	95	below_threshold
[Clostridium] fimetarium	strain=DSM 9179	GCA_900111235.1	99656	99656	type	True	76.2682	80	963	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:47,789] [INFO] DFAST Taxonomy check result was written to GCF_014287955.1_ASM1428795v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:47,790] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:47,790] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:47,791] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg234b814c-434f-400d-8733-3497a2a026b8/dqc_reference/checkm_data
[2024-01-24 11:12:47,792] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:47,830] [INFO] Task started: CheckM
[2024-01-24 11:12:47,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287955.1_ASM1428795v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287955.1_ASM1428795v1_genomic.fna/checkm_input GCF_014287955.1_ASM1428795v1_genomic.fna/checkm_result
[2024-01-24 11:13:13,910] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:13,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:13,929] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:13,929] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:13,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287955.1_ASM1428795v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:13,931] [INFO] Task started: Blastn
[2024-01-24 11:13:13,931] [INFO] Running command: blastn -query GCF_014287955.1_ASM1428795v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg234b814c-434f-400d-8733-3497a2a026b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287955.1_ASM1428795v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:15,127] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:15,130] [INFO] Selected 20 target genomes.
[2024-01-24 11:13:15,131] [INFO] Target genome list was writen to GCF_014287955.1_ASM1428795v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:15,162] [INFO] Task started: fastANI
[2024-01-24 11:13:15,162] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd65c54b-1126-4c5c-9d6e-3ba8264b1467/GCF_014287955.1_ASM1428795v1_genomic.fna.gz --refList GCF_014287955.1_ASM1428795v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287955.1_ASM1428795v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:25,080] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:25,098] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:25,098] [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_014287955.1	s__Lachnospira sp900316325	100.0	963	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.86	98.35	0.93	0.88	10	conclusive
GCF_003458705.1	s__Lachnospira sp003537285	80.7719	272	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.4867	98.01	96.87	0.87	0.80	8	-
GCA_900112995.1	s__Lachnospira rogosae_A	80.245	270	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.05	98.51	0.91	0.85	17	-
GCF_003464165.1	s__Lachnospira sp003451515	79.8103	238	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	97.95	97.44	0.88	0.84	9	-
GCF_018918265.1	s__Falcatimonas sp018918265	79.4832	141	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Falcatimonas	95.0	98.30	98.30	0.93	0.93	2	-
GCA_900547255.1	s__Lachnospira sp900547255	79.3484	246	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.87	99.87	0.91	0.91	2	-
GCA_900772425.1	s__Lachnospira sp900772425	78.996	128	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545725.1	s__Lachnospira sp900545725	78.5248	234	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.88	98.45	0.88	0.87	3	-
GCA_900552795.1	s__Lachnospira sp900552795	78.5188	200	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.54	99.07	0.90	0.84	3	-
GCA_000437735.1	s__Lachnospira sp000437735	78.4967	188	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.81	98.12	0.91	0.82	10	-
GCA_000436475.1	s__Lachnospira sp000436475	78.316	231	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	97.97	97.42	0.90	0.86	10	-
GCA_017626275.1	s__Lachnospira sp017626275	78.1461	98	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017397445.1	s__Lachnospira sp017397445	78.0667	142	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435585.1	s__Lachnospira sp002435585	78.0446	181	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363805.1	s__Eubacterium_G sp000434315	77.7998	94	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	98.14	0.87	0.84	6	-
GCA_910587485.1	s__Lachnospira sp910587485	77.7325	139	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002394205.1	s__Lachnospira sp002394205	77.6682	148	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.96	99.94	0.94	0.91	3	-
GCA_910585095.1	s__Lachnospira sp910585095	77.6336	133	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551945.1	s__Lachnospira sp900551945	77.4296	188	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	99.31	99.16	0.89	0.87	3	-
GCA_017935345.1	s__Coprococcus sp017935345	76.8559	60	963	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:25,100] [INFO] GTDB search result was written to GCF_014287955.1_ASM1428795v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:25,101] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:25,105] [INFO] DFAST_QC result json was written to GCF_014287955.1_ASM1428795v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:25,105] [INFO] DFAST_QC completed!
[2024-01-24 11:13:25,105] [INFO] Total running time: 0h1m1s