[2024-01-25 17:38:50,577] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:50,580] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:50,580] [INFO] DQC Reference Directory: /var/lib/cwl/stg53308cd6-97c9-4545-804d-35c2341ad723/dqc_reference
[2024-01-25 17:38:51,756] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:51,756] [INFO] Task started: Prodigal
[2024-01-25 17:38:51,757] [INFO] Running command: gunzip -c /var/lib/cwl/stg1b5bb8d6-6af0-44d9-bab9-e512d405c26e/GCF_027942795.1_ASM2794279v1_genomic.fna.gz | prodigal -d GCF_027942795.1_ASM2794279v1_genomic.fna/cds.fna -a GCF_027942795.1_ASM2794279v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:14,232] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:14,233] [INFO] Task started: HMMsearch
[2024-01-25 17:39:14,233] [INFO] Running command: hmmsearch --tblout GCF_027942795.1_ASM2794279v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53308cd6-97c9-4545-804d-35c2341ad723/dqc_reference/reference_markers.hmm GCF_027942795.1_ASM2794279v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:14,506] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:14,507] [INFO] Found 6/6 markers.
[2024-01-25 17:39:14,545] [INFO] Query marker FASTA was written to GCF_027942795.1_ASM2794279v1_genomic.fna/markers.fasta
[2024-01-25 17:39:14,546] [INFO] Task started: Blastn
[2024-01-25 17:39:14,546] [INFO] Running command: blastn -query GCF_027942795.1_ASM2794279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53308cd6-97c9-4545-804d-35c2341ad723/dqc_reference/reference_markers.fasta -out GCF_027942795.1_ASM2794279v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:15,142] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:15,146] [INFO] Selected 10 target genomes.
[2024-01-25 17:39:15,146] [INFO] Target genome list was writen to GCF_027942795.1_ASM2794279v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:15,151] [INFO] Task started: fastANI
[2024-01-25 17:39:15,151] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b5bb8d6-6af0-44d9-bab9-e512d405c26e/GCF_027942795.1_ASM2794279v1_genomic.fna.gz --refList GCF_027942795.1_ASM2794279v1_genomic.fna/target_genomes.txt --output GCF_027942795.1_ASM2794279v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:24,701] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:24,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53308cd6-97c9-4545-804d-35c2341ad723/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:24,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53308cd6-97c9-4545-804d-35c2341ad723/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:24,708] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 17:39:24,709] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 17:39:24,709] [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
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	99.504	1318	1572	95	inconclusive
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	95.8256	1106	1572	95	inconclusive
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	95.7939	1108	1572	95	inconclusive
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	95.7758	1095	1572	95	inconclusive
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	95.7272	1119	1572	95	inconclusive
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	93.8239	998	1572	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	91.8643	900	1572	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	83.7563	665	1572	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	81.2877	602	1572	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:24,710] [INFO] DFAST Taxonomy check result was written to GCF_027942795.1_ASM2794279v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:24,711] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:24,711] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:24,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53308cd6-97c9-4545-804d-35c2341ad723/dqc_reference/checkm_data
[2024-01-25 17:39:24,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:24,757] [INFO] Task started: CheckM
[2024-01-25 17:39:24,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027942795.1_ASM2794279v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027942795.1_ASM2794279v1_genomic.fna/checkm_input GCF_027942795.1_ASM2794279v1_genomic.fna/checkm_result
[2024-01-25 17:40:25,897] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:25,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:25,914] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:25,914] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:25,915] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027942795.1_ASM2794279v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:25,916] [INFO] Task started: Blastn
[2024-01-25 17:40:25,916] [INFO] Running command: blastn -query GCF_027942795.1_ASM2794279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53308cd6-97c9-4545-804d-35c2341ad723/dqc_reference/reference_markers_gtdb.fasta -out GCF_027942795.1_ASM2794279v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:26,825] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:26,829] [INFO] Selected 14 target genomes.
[2024-01-25 17:40:26,829] [INFO] Target genome list was writen to GCF_027942795.1_ASM2794279v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:26,848] [INFO] Task started: fastANI
[2024-01-25 17:40:26,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b5bb8d6-6af0-44d9-bab9-e512d405c26e/GCF_027942795.1_ASM2794279v1_genomic.fna.gz --refList GCF_027942795.1_ASM2794279v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027942795.1_ASM2794279v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:38,922] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:38,930] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:38,931] [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_000154205.1	s__Bacteroides uniformis	95.7796	1108	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.42	95.87	0.83	0.69	301	conclusive
GCF_000614125.1	s__Bacteroides rodentium	93.8408	997	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793475.1	s__Bacteroides sp002491635	91.5684	903	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.51	98.46	0.94	0.83	13	-
GCA_905197435.1	s__Bacteroides sp905197435	87.6829	636	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195635.1	s__Bacteroides fluxus	81.9784	669	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCF_000374365.1	s__Bacteroides gallinarum	81.8813	607	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCA_902388495.1	s__Bacteroides sp902388495	81.5346	669	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000154525.1	s__Bacteroides stercoris	81.3131	604	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.24	97.39	0.79	0.69	73	-
GCA_905203765.1	s__Bacteroides sp905203765	80.7283	512	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003438615.1	s__Bacteroides sp003545565	80.6938	569	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_004342845.1	s__Bacteroides heparinolyticus	79.9215	483	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.64	97.08	0.84	0.81	4	-
GCF_019129285.1	s__Bacteroides sp900552405	79.7468	544	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.09	95.34	0.92	0.76	12	-
GCA_905198575.1	s__Phocaeicola sp905198575	77.4844	82	1572	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:38,932] [INFO] GTDB search result was written to GCF_027942795.1_ASM2794279v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:38,932] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:38,935] [INFO] DFAST_QC result json was written to GCF_027942795.1_ASM2794279v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:38,935] [INFO] DFAST_QC completed!
[2024-01-25 17:40:38,935] [INFO] Total running time: 0h1m48s