[2023-06-30 03:57:01,128] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:57:01,131] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:57:01,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg6de66e14-a09d-4830-96ef-058a7ba854a7/dqc_reference
[2023-06-30 03:57:03,398] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:57:03,399] [INFO] Task started: Prodigal
[2023-06-30 03:57:03,400] [INFO] Running command: gunzip -c /var/lib/cwl/stg59ada332-bda0-4ede-b920-28a97ddd0137/GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna.gz | prodigal -d GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/cds.fna -a GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:57:32,280] [INFO] Task succeeded: Prodigal
[2023-06-30 03:57:32,280] [INFO] Task started: HMMsearch
[2023-06-30 03:57:32,280] [INFO] Running command: hmmsearch --tblout GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6de66e14-a09d-4830-96ef-058a7ba854a7/dqc_reference/reference_markers.hmm GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:57:32,565] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:57:32,567] [INFO] Found 6/6 markers.
[2023-06-30 03:57:32,612] [INFO] Query marker FASTA was written to GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/markers.fasta
[2023-06-30 03:57:32,613] [INFO] Task started: Blastn
[2023-06-30 03:57:32,613] [INFO] Running command: blastn -query GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/markers.fasta -db /var/lib/cwl/stg6de66e14-a09d-4830-96ef-058a7ba854a7/dqc_reference/reference_markers.fasta -out GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:57:33,286] [INFO] Task succeeded: Blastn
[2023-06-30 03:57:33,290] [INFO] Selected 9 target genomes.
[2023-06-30 03:57:33,291] [INFO] Target genome list was writen to GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/target_genomes.txt
[2023-06-30 03:57:33,293] [INFO] Task started: fastANI
[2023-06-30 03:57:33,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg59ada332-bda0-4ede-b920-28a97ddd0137/GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna.gz --refList GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/target_genomes.txt --output GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:57:40,536] [INFO] Task succeeded: fastANI
[2023-06-30 03:57:40,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6de66e14-a09d-4830-96ef-058a7ba854a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:57:40,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6de66e14-a09d-4830-96ef-058a7ba854a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:57:40,549] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:57:40,549] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:57:40,549] [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
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	77.6681	363	1591	95	below_threshold
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	77.4692	215	1591	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	77.2729	261	1591	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	76.9444	151	1591	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	76.8881	179	1591	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	76.8211	158	1591	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	74.754	71	1591	95	below_threshold
Streptomyces somaliensis	strain=DSM 40738	GCA_024349285.1	78355	78355	type	True	74.7069	52	1591	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	74.6294	95	1591	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:57:40,551] [INFO] DFAST Taxonomy check result was written to GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/tc_result.tsv
[2023-06-30 03:57:40,552] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:57:40,552] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:57:40,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6de66e14-a09d-4830-96ef-058a7ba854a7/dqc_reference/checkm_data
[2023-06-30 03:57:40,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:57:40,605] [INFO] Task started: CheckM
[2023-06-30 03:57:40,605] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/checkm_input GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/checkm_result
[2023-06-30 03:58:56,967] [INFO] Task succeeded: CheckM
[2023-06-30 03:58:56,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:58:56,993] [INFO] ===== Completeness check finished =====
[2023-06-30 03:58:56,993] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:58:56,994] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/markers.fasta)
[2023-06-30 03:58:56,994] [INFO] Task started: Blastn
[2023-06-30 03:58:56,994] [INFO] Running command: blastn -query GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/markers.fasta -db /var/lib/cwl/stg6de66e14-a09d-4830-96ef-058a7ba854a7/dqc_reference/reference_markers_gtdb.fasta -out GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:58:58,174] [INFO] Task succeeded: Blastn
[2023-06-30 03:58:58,180] [INFO] Selected 20 target genomes.
[2023-06-30 03:58:58,180] [INFO] Target genome list was writen to GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:58:58,184] [INFO] Task started: fastANI
[2023-06-30 03:58:58,185] [INFO] Running command: fastANI --query /var/lib/cwl/stg59ada332-bda0-4ede-b920-28a97ddd0137/GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna.gz --refList GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/target_genomes_gtdb.txt --output GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:59:14,841] [INFO] Task succeeded: fastANI
[2023-06-30 03:59:14,870] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:59:14,871] [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
GCA_903896015.1	s__CAITWF01 sp903896015	100.0	1585	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	99.72	99.39	0.95	0.93	8	conclusive
GCA_903840415.1	s__CAITWF01 sp903840415	80.5326	813	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	99.98	99.98	0.98	0.97	3	-
GCA_016235555.1	s__ER46 sp016235555	79.0589	738	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009695305.1	s__CAITWF01 sp009695305	79.0541	524	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794785.1	s__ER46 sp016794785	78.8157	540	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903948415.1	s__CAITWF01 sp903948415	78.7055	475	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903872505.1	s__Opi-474 sp903872505	78.564	357	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.99	99.98	0.99	0.99	3	-
GCA_903855985.1	s__Opi-474 sp903855985	78.5399	330	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.84	99.84	0.94	0.94	2	-
GCA_903862955.1	s__Opi-474 sp903862955	78.4396	359	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.96	99.95	0.97	0.97	5	-
GCA_002288455.1	s__ER46 sp002288455	78.3921	399	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903877135.1	s__Opitutus sp903877135	78.385	409	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	99.97	99.95	0.97	0.97	4	-
GCA_016794665.1	s__ER46 sp016794665	78.3486	457	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903881475.1	s__Opi-474 sp903881475	78.1101	320	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.50	98.31	0.92	0.83	9	-
GCA_903825285.1	s__Opi-474 sp903825285	77.9886	390	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.78	99.55	0.96	0.94	12	-
GCA_018239675.1	s__Opi-474 sp018239675	77.9377	307	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016217545.1	s__Didemnitutus sp016217545	77.8456	374	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019965.1	s__Opitutus terrae	77.6709	362	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903872425.1	s__CAIYUN01 sp903872425	77.3414	146	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIYUN01	95.0	99.72	99.70	0.88	0.87	3	-
GCA_005799525.1	s__CAITWF01 sp005799525	77.2771	282	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005792355.1	s__ER46 sp005792355	77.2448	378	1591	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	99.97	99.97	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-30 03:59:14,873] [INFO] GTDB search result was written to GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/result_gtdb.tsv
[2023-06-30 03:59:14,874] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:59:14,879] [INFO] DFAST_QC result json was written to GCA_903896015.1_freshwater_MAG_---_Umea2p1_bin-1006_genomic.fna/dqc_result.json
[2023-06-30 03:59:14,879] [INFO] DFAST_QC completed!
[2023-06-30 03:59:14,879] [INFO] Total running time: 0h2m14s