[2024-01-24 13:50:26,439] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:26,441] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:26,441] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7d687c4-7762-4881-ba6a-82a47023d9c0/dqc_reference
[2024-01-24 13:50:27,692] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:27,693] [INFO] Task started: Prodigal
[2024-01-24 13:50:27,693] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe3cf3b1-9978-4c62-b1ee-f39adfa061a9/GCF_900104635.1_PRJEB16356_genomic.fna.gz | prodigal -d GCF_900104635.1_PRJEB16356_genomic.fna/cds.fna -a GCF_900104635.1_PRJEB16356_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:36,850] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:36,851] [INFO] Task started: HMMsearch
[2024-01-24 13:50:36,851] [INFO] Running command: hmmsearch --tblout GCF_900104635.1_PRJEB16356_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7d687c4-7762-4881-ba6a-82a47023d9c0/dqc_reference/reference_markers.hmm GCF_900104635.1_PRJEB16356_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:37,127] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:37,128] [INFO] Found 6/6 markers.
[2024-01-24 13:50:37,168] [INFO] Query marker FASTA was written to GCF_900104635.1_PRJEB16356_genomic.fna/markers.fasta
[2024-01-24 13:50:37,169] [INFO] Task started: Blastn
[2024-01-24 13:50:37,169] [INFO] Running command: blastn -query GCF_900104635.1_PRJEB16356_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7d687c4-7762-4881-ba6a-82a47023d9c0/dqc_reference/reference_markers.fasta -out GCF_900104635.1_PRJEB16356_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:37,831] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:37,840] [INFO] Selected 20 target genomes.
[2024-01-24 13:50:37,841] [INFO] Target genome list was writen to GCF_900104635.1_PRJEB16356_genomic.fna/target_genomes.txt
[2024-01-24 13:50:37,908] [INFO] Task started: fastANI
[2024-01-24 13:50:37,908] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe3cf3b1-9978-4c62-b1ee-f39adfa061a9/GCF_900104635.1_PRJEB16356_genomic.fna.gz --refList GCF_900104635.1_PRJEB16356_genomic.fna/target_genomes.txt --output GCF_900104635.1_PRJEB16356_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:47,914] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:47,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7d687c4-7762-4881-ba6a-82a47023d9c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:47,915] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7d687c4-7762-4881-ba6a-82a47023d9c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:47,937] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:47,937] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:47,937] [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
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	100.0	1196	1196	95	conclusive
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	84.1143	188	1196	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	82.5975	176	1196	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	80.9013	231	1196	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	80.623	223	1196	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	80.5872	222	1196	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	80.4008	220	1196	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	80.2453	123	1196	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	80.1664	204	1196	95	below_threshold
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	80.1134	205	1196	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	79.7451	198	1196	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	79.3989	127	1196	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	79.3983	150	1196	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	79.0068	150	1196	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	78.7647	146	1196	95	below_threshold
Bariatricus massiliensis	strain=AT12	GCA_900086725.1	1745713	1745713	type	True	78.7193	107	1196	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	78.5772	122	1196	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	78.2946	128	1196	95	below_threshold
Sellimonas intestinalis	strain=BR72	GCA_001280875.1	1653434	1653434	type	True	77.5462	110	1196	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:47,939] [INFO] DFAST Taxonomy check result was written to GCF_900104635.1_PRJEB16356_genomic.fna/tc_result.tsv
[2024-01-24 13:50:47,940] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:47,940] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:47,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7d687c4-7762-4881-ba6a-82a47023d9c0/dqc_reference/checkm_data
[2024-01-24 13:50:47,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:47,980] [INFO] Task started: CheckM
[2024-01-24 13:50:47,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104635.1_PRJEB16356_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104635.1_PRJEB16356_genomic.fna/checkm_input GCF_900104635.1_PRJEB16356_genomic.fna/checkm_result
[2024-01-24 13:51:20,208] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:20,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:20,232] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:20,232] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:20,233] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104635.1_PRJEB16356_genomic.fna/markers.fasta)
[2024-01-24 13:51:20,233] [INFO] Task started: Blastn
[2024-01-24 13:51:20,233] [INFO] Running command: blastn -query GCF_900104635.1_PRJEB16356_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7d687c4-7762-4881-ba6a-82a47023d9c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104635.1_PRJEB16356_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:21,328] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:21,332] [INFO] Selected 17 target genomes.
[2024-01-24 13:51:21,332] [INFO] Target genome list was writen to GCF_900104635.1_PRJEB16356_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:21,447] [INFO] Task started: fastANI
[2024-01-24 13:51:21,448] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe3cf3b1-9978-4c62-b1ee-f39adfa061a9/GCF_900104635.1_PRJEB16356_genomic.fna.gz --refList GCF_900104635.1_PRJEB16356_genomic.fna/target_genomes_gtdb.txt --output GCF_900104635.1_PRJEB16356_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:29,760] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:29,780] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:29,781] [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_900104635.1	s__Faecalimonas phoceensis	100.0	1196	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	98.10	95.01	0.81	0.60	21	conclusive
GCF_018228665.1	s__UBA9414 sp003458885	81.6099	191	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	97.84	97.84	0.85	0.85	3	-
GCF_008121495.1	s__Ruminococcus_B gnavus	80.8808	229	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	98.58	96.13	0.80	0.66	102	-
GCA_902381685.1	s__Faecalimonas sp000209385	80.556	200	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	99.49	98.98	0.93	0.86	3	-
GCA_018365895.1	s__UBA9414 sp018365895	79.8082	150	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551895.1	s__Faecalimonas sp900551895	79.7827	151	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	98.69	98.58	0.83	0.80	3	-
GCF_004346095.1	s__Faecalimonas umbilicata	79.7522	197	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	98.30	97.78	0.83	0.78	20	-
GCF_012524165.2	s__Muricomes sp012524165	79.3831	151	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017472665.1	s__Faecalimonas sp017472665	78.4712	115	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017416155.1	s__Faecalimonas sp017416155	78.4694	130	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465565.1	s__Faecalimonas sp017465565	78.4516	157	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550235.1	s__Faecalimonas sp900550235	78.2399	147	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905197485.1	s__Faecalimonas sp900555395	78.1414	152	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	100.00	100.00	0.94	0.94	2	-
GCA_900556835.1	s__Faecalimonas sp900556835	78.0975	140	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900765975.1	s__Schaedlerella sp900765975	77.7976	113	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.94	99.94	0.80	0.80	2	-
GCA_016295505.1	s__Dorea_A sp016295505	76.911	98	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905209865.1	s__Mediterraneibacter sp900752395	76.8064	92	1196	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.94	99.94	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:29,782] [INFO] GTDB search result was written to GCF_900104635.1_PRJEB16356_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:29,783] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:29,788] [INFO] DFAST_QC result json was written to GCF_900104635.1_PRJEB16356_genomic.fna/dqc_result.json
[2024-01-24 13:51:29,788] [INFO] DFAST_QC completed!
[2024-01-24 13:51:29,788] [INFO] Total running time: 0h1m3s