[2023-06-28 05:23:13,188] [INFO] DFAST_QC pipeline started.
[2023-06-28 05:23:13,190] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 05:23:13,190] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf1a5e5f-82f3-47d6-aa50-3ee3bd7c03b4/dqc_reference
[2023-06-28 05:23:15,017] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 05:23:15,018] [INFO] Task started: Prodigal
[2023-06-28 05:23:15,019] [INFO] Running command: gunzip -c /var/lib/cwl/stg65ae675a-fa37-4117-bc42-065dcf6ae213/GCA_944320955.1_E27_bin52_genomic.fna.gz | prodigal -d GCA_944320955.1_E27_bin52_genomic.fna/cds.fna -a GCA_944320955.1_E27_bin52_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 05:23:29,780] [INFO] Task succeeded: Prodigal
[2023-06-28 05:23:29,781] [INFO] Task started: HMMsearch
[2023-06-28 05:23:29,781] [INFO] Running command: hmmsearch --tblout GCA_944320955.1_E27_bin52_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf1a5e5f-82f3-47d6-aa50-3ee3bd7c03b4/dqc_reference/reference_markers.hmm GCA_944320955.1_E27_bin52_genomic.fna/protein.faa > /dev/null
[2023-06-28 05:23:29,974] [INFO] Task succeeded: HMMsearch
[2023-06-28 05:23:29,975] [INFO] Found 6/6 markers.
[2023-06-28 05:23:29,997] [INFO] Query marker FASTA was written to GCA_944320955.1_E27_bin52_genomic.fna/markers.fasta
[2023-06-28 05:23:29,997] [INFO] Task started: Blastn
[2023-06-28 05:23:29,997] [INFO] Running command: blastn -query GCA_944320955.1_E27_bin52_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf1a5e5f-82f3-47d6-aa50-3ee3bd7c03b4/dqc_reference/reference_markers.fasta -out GCA_944320955.1_E27_bin52_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:23:30,559] [INFO] Task succeeded: Blastn
[2023-06-28 05:23:30,563] [INFO] Selected 32 target genomes.
[2023-06-28 05:23:30,563] [INFO] Target genome list was writen to GCA_944320955.1_E27_bin52_genomic.fna/target_genomes.txt
[2023-06-28 05:23:30,564] [INFO] Task started: fastANI
[2023-06-28 05:23:30,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg65ae675a-fa37-4117-bc42-065dcf6ae213/GCA_944320955.1_E27_bin52_genomic.fna.gz --refList GCA_944320955.1_E27_bin52_genomic.fna/target_genomes.txt --output GCA_944320955.1_E27_bin52_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 05:23:52,787] [INFO] Task succeeded: fastANI
[2023-06-28 05:23:52,788] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf1a5e5f-82f3-47d6-aa50-3ee3bd7c03b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 05:23:52,788] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf1a5e5f-82f3-47d6-aa50-3ee3bd7c03b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 05:23:52,795] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 05:23:52,795] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 05:23:52,795] [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 rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	77.0603	56	866	95	below_threshold
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	76.3924	63	866	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.0733	66	866	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.0553	67	866	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.0392	75	866	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	76.002	55	866	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	75.9544	55	866	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 05:23:52,797] [INFO] DFAST Taxonomy check result was written to GCA_944320955.1_E27_bin52_genomic.fna/tc_result.tsv
[2023-06-28 05:23:52,798] [INFO] ===== Taxonomy check completed =====
[2023-06-28 05:23:52,798] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 05:23:52,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf1a5e5f-82f3-47d6-aa50-3ee3bd7c03b4/dqc_reference/checkm_data
[2023-06-28 05:23:52,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 05:23:52,826] [INFO] Task started: CheckM
[2023-06-28 05:23:52,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320955.1_E27_bin52_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320955.1_E27_bin52_genomic.fna/checkm_input GCA_944320955.1_E27_bin52_genomic.fna/checkm_result
[2023-06-28 05:24:34,131] [INFO] Task succeeded: CheckM
[2023-06-28 05:24:34,132] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 05:24:34,148] [INFO] ===== Completeness check finished =====
[2023-06-28 05:24:34,148] [INFO] ===== Start GTDB Search =====
[2023-06-28 05:24:34,148] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320955.1_E27_bin52_genomic.fna/markers.fasta)
[2023-06-28 05:24:34,149] [INFO] Task started: Blastn
[2023-06-28 05:24:34,149] [INFO] Running command: blastn -query GCA_944320955.1_E27_bin52_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf1a5e5f-82f3-47d6-aa50-3ee3bd7c03b4/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320955.1_E27_bin52_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 05:24:34,958] [INFO] Task succeeded: Blastn
[2023-06-28 05:24:34,969] [INFO] Selected 31 target genomes.
[2023-06-28 05:24:34,969] [INFO] Target genome list was writen to GCA_944320955.1_E27_bin52_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 05:24:35,029] [INFO] Task started: fastANI
[2023-06-28 05:24:35,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg65ae675a-fa37-4117-bc42-065dcf6ae213/GCA_944320955.1_E27_bin52_genomic.fna.gz --refList GCA_944320955.1_E27_bin52_genomic.fna/target_genomes_gtdb.txt --output GCA_944320955.1_E27_bin52_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 05:24:49,839] [INFO] Task succeeded: fastANI
[2023-06-28 05:24:49,853] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 05:24:49,853] [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_900128475.1	s__Bacteroides massiliensis	77.1692	154	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.63	97.57	0.90	0.85	6	-
GCA_019115825.1	s__Bacteroides pullicola	77.0532	117	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900015.1	s__Phocaeicola_A sp003489705	76.9146	87	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola_A	95.0	98.99	98.79	0.92	0.90	4	-
GCA_018714085.1	s__Alloprevotella pullistercoris	76.8347	67	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883785.1	s__Bacteroides intestinipullorum	76.8267	87	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130135.1	s__Bacteroides togonis	76.8039	99	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.34	96.94	0.82	0.80	8	-
GCA_000431275.1	s__Alloprevotella sp000431275	76.729	71	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.27	97.96	0.89	0.88	3	-
GCF_900291465.1	s__Phocaeicola_A sp900291465	76.7107	102	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola_A	95.0	97.97	97.87	0.87	0.85	4	-
GCA_017471925.1	s__Bacteroides sp017471925	76.5709	82	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017445145.1	s__UBA4372 sp017445145	76.5344	70	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004558305.1	s__Phocaeicola plebeius_B	76.4848	60	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017933995.1	s__Alloprevotella sp017933995	76.4147	68	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557185.1	s__Alloprevotella sp004557185	76.2442	66	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	98.58	98.39	0.90	0.87	3	-
GCA_017464815.1	s__Phocaeicola_A sp017464815	76.2147	75	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553815.1	s__Bacteroides sp900553815	76.1851	57	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.95	97.95	0.73	0.73	2	-
GCA_017455585.1	s__UBA4372 sp017455585	76.1157	52	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA4372	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004558535.1	s__Alloprevotella sp004558535	75.9518	55	866	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Alloprevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 05:24:49,855] [INFO] GTDB search result was written to GCA_944320955.1_E27_bin52_genomic.fna/result_gtdb.tsv
[2023-06-28 05:24:49,855] [INFO] ===== GTDB Search completed =====
[2023-06-28 05:24:49,858] [INFO] DFAST_QC result json was written to GCA_944320955.1_E27_bin52_genomic.fna/dqc_result.json
[2023-06-28 05:24:49,858] [INFO] DFAST_QC completed!
[2023-06-28 05:24:49,859] [INFO] Total running time: 0h1m37s