[2023-06-19 06:39:34,681] [INFO] DFAST_QC pipeline started.
[2023-06-19 06:39:34,685] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 06:39:34,685] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7371242-20ef-4bf9-a57e-3e9844044602/dqc_reference
[2023-06-19 06:39:36,973] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 06:39:36,975] [INFO] Task started: Prodigal
[2023-06-19 06:39:36,975] [INFO] Running command: gunzip -c /var/lib/cwl/stg1abb6d04-0a0a-4322-9a6f-385fbf27b1af/GCA_014871475.1_ASM1487147v1_genomic.fna.gz | prodigal -d GCA_014871475.1_ASM1487147v1_genomic.fna/cds.fna -a GCA_014871475.1_ASM1487147v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 06:39:59,033] [INFO] Task succeeded: Prodigal
[2023-06-19 06:39:59,033] [INFO] Task started: HMMsearch
[2023-06-19 06:39:59,033] [INFO] Running command: hmmsearch --tblout GCA_014871475.1_ASM1487147v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7371242-20ef-4bf9-a57e-3e9844044602/dqc_reference/reference_markers.hmm GCA_014871475.1_ASM1487147v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 06:39:59,285] [INFO] Task succeeded: HMMsearch
[2023-06-19 06:39:59,287] [INFO] Found 6/6 markers.
[2023-06-19 06:39:59,321] [INFO] Query marker FASTA was written to GCA_014871475.1_ASM1487147v1_genomic.fna/markers.fasta
[2023-06-19 06:39:59,322] [INFO] Task started: Blastn
[2023-06-19 06:39:59,322] [INFO] Running command: blastn -query GCA_014871475.1_ASM1487147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7371242-20ef-4bf9-a57e-3e9844044602/dqc_reference/reference_markers.fasta -out GCA_014871475.1_ASM1487147v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:39:59,906] [INFO] Task succeeded: Blastn
[2023-06-19 06:39:59,910] [INFO] Selected 9 target genomes.
[2023-06-19 06:39:59,911] [INFO] Target genome list was writen to GCA_014871475.1_ASM1487147v1_genomic.fna/target_genomes.txt
[2023-06-19 06:39:59,912] [INFO] Task started: fastANI
[2023-06-19 06:39:59,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg1abb6d04-0a0a-4322-9a6f-385fbf27b1af/GCA_014871475.1_ASM1487147v1_genomic.fna.gz --refList GCA_014871475.1_ASM1487147v1_genomic.fna/target_genomes.txt --output GCA_014871475.1_ASM1487147v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 06:40:07,911] [INFO] Task succeeded: fastANI
[2023-06-19 06:40:07,912] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7371242-20ef-4bf9-a57e-3e9844044602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 06:40:07,912] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7371242-20ef-4bf9-a57e-3e9844044602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 06:40:07,923] [INFO] Found 8 fastANI hits (5 hits with ANI > threshold)
[2023-06-19 06:40:07,924] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-19 06:40:07,924] [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	99.0134	1161	1272	95	inconclusive
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	96.1106	1038	1272	95	inconclusive
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	96.0938	1037	1272	95	inconclusive
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	96.0738	1030	1272	95	inconclusive
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	96.0629	1034	1272	95	inconclusive
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	91.8506	840	1272	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	80.4676	547	1272	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	79.9482	501	1272	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 06:40:07,926] [INFO] DFAST Taxonomy check result was written to GCA_014871475.1_ASM1487147v1_genomic.fna/tc_result.tsv
[2023-06-19 06:40:07,926] [INFO] ===== Taxonomy check completed =====
[2023-06-19 06:40:07,926] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 06:40:07,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7371242-20ef-4bf9-a57e-3e9844044602/dqc_reference/checkm_data
[2023-06-19 06:40:07,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 06:40:07,968] [INFO] Task started: CheckM
[2023-06-19 06:40:07,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014871475.1_ASM1487147v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014871475.1_ASM1487147v1_genomic.fna/checkm_input GCA_014871475.1_ASM1487147v1_genomic.fna/checkm_result
[2023-06-19 06:41:09,160] [INFO] Task succeeded: CheckM
[2023-06-19 06:41:09,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 06:41:09,186] [INFO] ===== Completeness check finished =====
[2023-06-19 06:41:09,186] [INFO] ===== Start GTDB Search =====
[2023-06-19 06:41:09,187] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014871475.1_ASM1487147v1_genomic.fna/markers.fasta)
[2023-06-19 06:41:09,187] [INFO] Task started: Blastn
[2023-06-19 06:41:09,187] [INFO] Running command: blastn -query GCA_014871475.1_ASM1487147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7371242-20ef-4bf9-a57e-3e9844044602/dqc_reference/reference_markers_gtdb.fasta -out GCA_014871475.1_ASM1487147v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:41:10,043] [INFO] Task succeeded: Blastn
[2023-06-19 06:41:10,048] [INFO] Selected 12 target genomes.
[2023-06-19 06:41:10,048] [INFO] Target genome list was writen to GCA_014871475.1_ASM1487147v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 06:41:10,049] [INFO] Task started: fastANI
[2023-06-19 06:41:10,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg1abb6d04-0a0a-4322-9a6f-385fbf27b1af/GCA_014871475.1_ASM1487147v1_genomic.fna.gz --refList GCA_014871475.1_ASM1487147v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014871475.1_ASM1487147v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 06:41:19,863] [INFO] Task succeeded: fastANI
[2023-06-19 06:41:19,877] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 06:41:19,877] [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	96.0776	1038	1272	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	93.9888	925	1272	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	91.7129	834	1272	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	87.7355	610	1272	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	81.5727	618	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.66	99.32	0.94	0.88	3	-
GCA_902388495.1	s__Bacteroides sp902388495	81.438	640	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.98	0.98	2	-
GCA_905203765.1	s__Bacteroides sp905203765	80.7411	505	1272	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	80.0195	499	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.56	99.02	0.91	0.88	7	-
GCF_000374365.1	s__Bacteroides gallinarum	79.9496	505	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
GCF_019129285.1	s__Bacteroides sp900552405	79.213	494	1272	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	77.4536	79	1272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 06:41:19,879] [INFO] GTDB search result was written to GCA_014871475.1_ASM1487147v1_genomic.fna/result_gtdb.tsv
[2023-06-19 06:41:19,880] [INFO] ===== GTDB Search completed =====
[2023-06-19 06:41:19,883] [INFO] DFAST_QC result json was written to GCA_014871475.1_ASM1487147v1_genomic.fna/dqc_result.json
[2023-06-19 06:41:19,884] [INFO] DFAST_QC completed!
[2023-06-19 06:41:19,884] [INFO] Total running time: 0h1m45s