[2024-01-25 20:26:35,842] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:26:35,846] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:26:35,846] [INFO] DQC Reference Directory: /var/lib/cwl/stgbddce7cc-159e-4705-8c14-cbd95a3f3f13/dqc_reference
[2024-01-25 20:26:37,000] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:26:37,001] [INFO] Task started: Prodigal
[2024-01-25 20:26:37,001] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fac3765-03c8-43e6-8862-096802ef1750/GCF_900128455.1_PRJEB18046_genomic.fna.gz | prodigal -d GCF_900128455.1_PRJEB18046_genomic.fna/cds.fna -a GCF_900128455.1_PRJEB18046_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:26:56,540] [INFO] Task succeeded: Prodigal
[2024-01-25 20:26:56,540] [INFO] Task started: HMMsearch
[2024-01-25 20:26:56,540] [INFO] Running command: hmmsearch --tblout GCF_900128455.1_PRJEB18046_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbddce7cc-159e-4705-8c14-cbd95a3f3f13/dqc_reference/reference_markers.hmm GCF_900128455.1_PRJEB18046_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:26:56,767] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:26:56,769] [INFO] Found 6/6 markers.
[2024-01-25 20:26:56,827] [INFO] Query marker FASTA was written to GCF_900128455.1_PRJEB18046_genomic.fna/markers.fasta
[2024-01-25 20:26:56,827] [INFO] Task started: Blastn
[2024-01-25 20:26:56,827] [INFO] Running command: blastn -query GCF_900128455.1_PRJEB18046_genomic.fna/markers.fasta -db /var/lib/cwl/stgbddce7cc-159e-4705-8c14-cbd95a3f3f13/dqc_reference/reference_markers.fasta -out GCF_900128455.1_PRJEB18046_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:57,398] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:57,400] [INFO] Selected 13 target genomes.
[2024-01-25 20:26:57,401] [INFO] Target genome list was writen to GCF_900128455.1_PRJEB18046_genomic.fna/target_genomes.txt
[2024-01-25 20:26:57,427] [INFO] Task started: fastANI
[2024-01-25 20:26:57,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fac3765-03c8-43e6-8862-096802ef1750/GCF_900128455.1_PRJEB18046_genomic.fna.gz --refList GCF_900128455.1_PRJEB18046_genomic.fna/target_genomes.txt --output GCF_900128455.1_PRJEB18046_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:27:06,677] [INFO] Task succeeded: fastANI
[2024-01-25 20:27:06,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbddce7cc-159e-4705-8c14-cbd95a3f3f13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:27:06,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbddce7cc-159e-4705-8c14-cbd95a3f3f13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:27:06,687] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:27:06,687] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:27:06,687] [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
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	84.0766	811	1349	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	80.5443	455	1349	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	80.5224	454	1349	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	80.2492	403	1349	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	80.0134	368	1349	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	79.9838	371	1349	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	79.741	303	1349	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	79.2916	331	1349	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	79.0884	206	1349	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	79.0742	205	1349	95	below_threshold
Bacteroides fluxus	strain=YIT 12057	GCA_000195635.1	626930	626930	type	True	78.4778	178	1349	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	78.4455	183	1349	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	78.1807	179	1349	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:27:06,689] [INFO] DFAST Taxonomy check result was written to GCF_900128455.1_PRJEB18046_genomic.fna/tc_result.tsv
[2024-01-25 20:27:06,690] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:27:06,690] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:27:06,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbddce7cc-159e-4705-8c14-cbd95a3f3f13/dqc_reference/checkm_data
[2024-01-25 20:27:06,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:27:06,733] [INFO] Task started: CheckM
[2024-01-25 20:27:06,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900128455.1_PRJEB18046_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900128455.1_PRJEB18046_genomic.fna/checkm_input GCF_900128455.1_PRJEB18046_genomic.fna/checkm_result
[2024-01-25 20:28:00,797] [INFO] Task succeeded: CheckM
[2024-01-25 20:28:00,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:28:00,818] [INFO] ===== Completeness check finished =====
[2024-01-25 20:28:00,818] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:28:00,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900128455.1_PRJEB18046_genomic.fna/markers.fasta)
[2024-01-25 20:28:00,819] [INFO] Task started: Blastn
[2024-01-25 20:28:00,819] [INFO] Running command: blastn -query GCF_900128455.1_PRJEB18046_genomic.fna/markers.fasta -db /var/lib/cwl/stgbddce7cc-159e-4705-8c14-cbd95a3f3f13/dqc_reference/reference_markers_gtdb.fasta -out GCF_900128455.1_PRJEB18046_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:28:01,668] [INFO] Task succeeded: Blastn
[2024-01-25 20:28:01,671] [INFO] Selected 8 target genomes.
[2024-01-25 20:28:01,671] [INFO] Target genome list was writen to GCF_900128455.1_PRJEB18046_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:28:01,680] [INFO] Task started: fastANI
[2024-01-25 20:28:01,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fac3765-03c8-43e6-8862-096802ef1750/GCF_900128455.1_PRJEB18046_genomic.fna.gz --refList GCF_900128455.1_PRJEB18046_genomic.fna/target_genomes_gtdb.txt --output GCF_900128455.1_PRJEB18046_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:28:08,603] [INFO] Task succeeded: fastANI
[2024-01-25 20:28:08,610] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:28:08,610] [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_900128455.1	s__Phocaeicola mediterraneensis	100.0	1349	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.66	98.61	0.84	0.80	3	conclusive
GCA_900551445.1	s__Phocaeicola sp900551445	93.8854	727	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.87	97.79	0.75	0.72	3	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	91.8858	916	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCA_900552075.1	s__Phocaeicola sp900552075	91.2496	680	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900355.1	s__Phocaeicola sp900551065	89.6653	893	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	96.34	95.04	0.86	0.84	4	-
GCF_000187895.1	s__Phocaeicola plebeius	84.0579	813	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCF_003437535.1	s__Phocaeicola plebeius_A	83.7087	816	1349	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
GCA_019120125.1	s__Phocaeicola excrementigallinarum	78.4265	332	1349	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 20:28:08,611] [INFO] GTDB search result was written to GCF_900128455.1_PRJEB18046_genomic.fna/result_gtdb.tsv
[2024-01-25 20:28:08,612] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:28:08,614] [INFO] DFAST_QC result json was written to GCF_900128455.1_PRJEB18046_genomic.fna/dqc_result.json
[2024-01-25 20:28:08,614] [INFO] DFAST_QC completed!
[2024-01-25 20:28:08,614] [INFO] Total running time: 0h1m33s